SnapGene Changelog

What's new in SnapGene 7.2.0

Mar 28, 2024

Features and Enhancements:
Primer homodimers
Calculation of primer homodimer structures using the RNAcofold tool from the Vienna RNA package
Visualize primer homodimers colored by sequence or confidence
Tabbed file window enhancements
Enabled dragging file tabs in and out of a window
Added ability to have multiple windows containing file tabs
Tabbed file windows can now exist without a “Project” panel
Added current filename to the top toolbar
Improved visibility of selected tab
Enhancements to data management within the Project interface
Enabled importing files directly into subfolders
Added a drop indicator to signify that files can be imported into Projects by drag and drop
Added Expand/Collapse All Folders commands to the file panel actions menu
Added an Open File command to the context menu shown when right-clicking a single file in the file panel.
Allow opening PDFs in a Project by double-clicking
Enhancements to chromatogram trace file view settings
Adjusted default height so that peaks are not stretched within tabbed windows
Display peak information when mousing over quality data
Display base highlighting when mousing over trace file sequences
Updated defaults for In-Fusion cloning to use a 20 bp fragment when there are multiple fragments, as per the updated recommendations from Takara Bio
Added BioGate ladders (100 bp, 100 bp Plus, and 1 KB) for agarose gel simulations
Added GeneAll GENESTA ladders (100 bp, 250 bp, and 1 kb) for agarose gel simulations
Added Hylabs ladders (50 bp, 100 bp, and 1 KB+) for agarose gel simulations
Updates to Standard common features database
Added the Anderson Constitutive promoter set
Added alternative Bxb1 integrase and associated sites
Added mCyRFP, mScarlet3, StayGold, and mStayGold Fluorescent Protein features
Updated Csy4 and human U6 promoter sequences
Added a ssDNA file to the Sample Project
Additional Changes and Fixes:
Improved performance by avoiding recomputing alignment to a reference DNA sequence when edits are made to the reference or aligned sequences
Added progress dialog and allow canceling aligning to a reference DNA sequence
Allow user to specify the quality format if it is ambiguous when importing FASTQ sequencing reads
Added a side toolbar to the secondary structure view
Improved the appearance of the Edit DNA Ends dialog when using dark mode
Removed the option to copy bottom strand bases that were erroneously shown when viewing a protein alignment
Enable opening non-native files by right-clicking file names in the folder panel
Expanded the click area in the Choose Enzymes dialog so that options may be selected by clicking on labels to the right of radio buttons
Improved behavior to avoid unnecessarily showing the main Project window when the “Open files in a separate window by default” preference is enabled
Translated examples in file search fields
Fixed a bug whereby assemble contigs was used in an inconsistent default location for results to be stored (Project folder or Collection) depending on the ‘open files in separate windows setting’
Fixed a crash which occurred when canceling detecting common features on multiple files in a collection
Fixed a crash which could occur when running file searches in the Project panel
Fixed a crash that could occur when searching for a region that spans the origin
Fixed a bug that made it impossible to resurrect an ancestor after running bulk edits in Collections
Fixed an error that prevented simulating Gateway cloning using sites that span the numerical origin
Fixed the enzyme database to show buffer values containing < symbol
Fixed the alignment of labels in multiple sequence alignments side panel
Trimmed white space added to the start or end of the email address field
Enabled the New File pane to be shown on Windows when using a smaller screen
Ensure features within the amplified region are transferred to the product when simulating PCR using primers that overlap and include internal insertions or replacements.
Fixed an issue on Windows where amplified fragments disappear in the amplified fragments list depending on which fragment was selected.
Ensure files double-clicked in the Finder or Windows Explorer are opened full screen if the associated option is checked in Preferences
Default to the opened project when choosing where to save imported files
Reduced the minimum width required for file tabs and improved their look and feel when there are a large number of tabs or space is otherwise limited
Ensure chromatogram quality is printed if it is toggled on
Improved stability when opening files
Corrected the uracil count when using Show RNA Calculations
Added a progress indicator and allow canceling aligning to a reference if it is taking a long time
Removed “Show Structure” buttons from the Import Primers dialog
Ensure recently closed tabs are opened in the current window and not a separate window even if the “Open files in separate windows by default” preference is checked
Fixed an issue where the Golden Gate Cloning dialog could change when accepting out of the adjust overhangs dialog if only one option is available
Ensure the vector's numerical origin is restored in the assembled product if the vector is digested directly
Improved performance when working with many tabs
Fixed an issue with importing files into a project by dropping them on a selected folder
Ensure vector features are transferred to the product when inserting a restriction fragment
Fixed an issue that could prevent simulating inserting a restriction fragment
Optimized performance when detecting sequence topology when creating new files, adding common features, and refining feature colors during import of non-native files
Implemented new algorithms for searching and indexing sequences, which replace the MICA algorithm, and optimized their performance for core molecular biology use cases
Reduced file size for newly created and edited files

New in SnapGene 7.1.2 (Mar 3, 2024)

New in SnapGene 7.1.1 (Dec 28, 2023)

New in SnapGene 7.0.3 (Oct 12, 2023)

New in SnapGene 7.0.2 (Jul 27, 2023)

Enhancements:
Reduced the size of icons in the top toolbar by default
Improved look and feel of tabs in search dialog
Improved find dialog drop shadow
Fixes:
Fixed a bug that resulted in files and folders that with non-latin characters sometimes appearing not writable when in fact they are.
Fixed a bug where dragging out a selection in map view would stop working after passing over an annotation
Fixed issues with adjusting segment ranges for split features
Fixed selecting mirror files created by previously importing a Vector NTI database
Fixed opening some SeqBuilder files
Fixed importing Geneious files that contain a mixture of sequence types
Fixed a crash that could occur when changing the sequence typology in the New File dialog
Fixed a crash when opening some non-native (e.g. GenBank) files
Improve stability when working with collections
Improved stability when popping a stand-alone window back into a tab
Various other stability fixes
Fixed a bug that resulted in the undo, redo, cut, copy and paste menu actions incorrectly being disabled when using the New File dialog
Fixed an issue that sometimes prevented switching tabs using keyboard shortcuts
Fixed detecting if restriction sites at the numerical origin is methylation sensitive
Fixed displaying quality data in FASTQ files
Fixed a bug where residues in ssRNA secondary structures were not numbered consistent with the sequence numbering
Editing search query no longer triggers a new search unless the change leads to a logical change to the search query
Improved layout and scrolling of content in the search dialog
Support top toolbar menu actions for all file types
Restore the visible state (shown or hidden) of the top toolbar
When popping tabs out respect the "Open windows full screen by default" preference
Fix opening a collection when double-clicking an "Open this collection" file in the folder panel
Fix various minor visual glitches with the search dialog
Fixed a bug that resulted in text being clipped or ellided when using the Japanese translation
Fixed a bug that prevented a number of messages from being translated to Chinese or Japanese
Fixed a bug that prevented pasting into the search dialog query when viewing a chromatogram or an agarose gel
Fixed a bug where buttons could continue to be appear to be moused over after the mouse moves away
Files imported into an agarose gel or an alignment are now listed in the same order as in the folder view
Fixed a bug that sometimes prevented making selections on older macOS versions by disabling hiding the top toolbar
Ensure existing files with the same name are not overwritten when performing a contig assembly
Fixed a bug that sometimes prevented selecting the relevant amplified fragment when clicking a primer binding sites while viewing an agarose gel
Fixed a bug that prevented showing file icons for selected non-native files in the folder panel

New in SnapGene 7.0.1 (Jun 21, 2023)

Enhancements:
Added a 600 ms delay before the collapsed sidebar pops over on mouseover.
Reduced the visual footprint of the top toolbar
Added support for dragging files from the folder view into the simulate agarose gel dialog
Streamlined applying enzymes and primers to other agarose gel lanes by automatically switching the preparation method
Added a context menu to the search field in the search dialog
Improved presentation of searching and search results and links to all results in the search dialog
Improved tooltip for close tab buttons
Fixes:
Improved stability
Fixed various issues with selecting tabs
Fixed an issue that prevented reliably popping out tabs on macOS
Fixed an issue that made it difficult to close files on some read only remote volumes
Improved placement of menus when clicking kebab buttons so they do not extend off the screen or are shown in the wrong display.
Fixed a bug where the wrong document might be shown when selecting a tab if previously none were selected
Fixed an issue that resulted in broken aliases when importing a Vector NTI database
Fixed an issue that sometimes resulted in action dialogs not updating the product when a primer was modified
Fixed an issue that could result in a simulated product showing up blank in cloning dialogs
Fixed various issues with flagging terms with problems when using the search dialog
Fixed an issue where clicking suggested terms and examples could result in duplicate terms be inserted into the query
Fixed an issue that made it difficult to clear the query in the search dialog
Fixed an issue that prevented clicking the X buttons repeatedly without moving the mouse in order to quickly clear out recent documents and projects
Enable the top toolbar menu actions in the View menu when the Get Started pane is shown
Fixed a issue that prevented importing some Uniprot sequences if a similar sequence exists in the nucleotide database
Fixed an issue that could result in primers being added to the wrong document.
Fixed a bug that could result in the detect common features checkbox becoming unchecked when modifying the sequence in the New File dialog.
Improved stability when switching between documents in a collection.
Fixed a crash that could occur when simulating an agarose gel
Fixed issues various with using cut, copy and paste in the search dialog
Improved the positioning of the advanced search dialog
Fixed an issue that resulted in charms at the top left being clipped when the sidebar was collapsed on Windows
Fixed an issue where changing topology or strandedness in the New File pane resulted in the preview turning blank and detected features not being shown
Fixed varius rendering artifacts when viewing the Get Started pane with SnapGene Viewer
Fixed an issue where if multiple tabs with unsaved changes are open, the active tab was not always used in cloning dialogs
Fixed an issue that resulted in always opening standard cloning vector as a stand alone window instead of a tab
Ensure orientation controls in cloning dialogs work reliably
Improved text colors for status widgets in light and dark modes
Fixed an issue where export options for gels could be listed in the File menu after switching to other document types
Fixed a freeze when changing topology in the Design Synthetic Construct dialog
Disabled the Order Construct menu actions when viewing the Get Started pane
Prevent primer name conflicts when manually specifying primers in an agarose gel
Prevent primer name conflicts when applying primers to all lanes in an agarose gel
Fixed an issue where some buttons would show pliancy, suggesting they could be clicked, when the mouse was outside the button area.
Fixed a bug that could result in spaces being inserted into the query when switching to the advanced search dialog.
Improved link to learn more about how to manage your projects in SnapGene
Fixed a bug where when using the context menu to pop out a tab as a new window did not result in the window being active.
Fixed a bug where clicking the advanced search button on Windows did not result in showing the advanced search dialog, only the result results tab.
Fixed various issues with showning pliancy after popping out a window.

New in SnapGene 7.0.0 (Jun 7, 2023)

SnapGene 7.0 introduces an updated look and feel with enhanced data management capabilities. Easily navigate files and folders with tabs, and perform sequence and metadata based searches for files directly from the new folder panel. Other enhancements include new primer insertion annotations and various usability improvements.
Tabbed Interface:
Navigate between documents using the new tabbed interface, or pop out documents into separate windows for comparison purposes.
File and Folder Management:
Choose any folder on your file system as a project and quickly view subfolders and files directly within a new, collapsible, folder panel. Perform standard file operations and quickly browse all supported file types.
File Search:
Quickly find files within a project using attributes such as the name or type, containing sequence, feature annotations and more via a flexible, modern interface.
Primer Annotations:
Visualize insertions such as enzymes, codon or short peptide sequences added to your primers in the updated Add/Edit Primer dialog. Regions of interest (Golden Gate restriction sites, Gateway cloning attB sites, directional TOPO motif) are now annotated for primers designed automatically as well.
Preview Detected Features for New Sequences
The new file pane now includes a sequence map to preview features that are detected in your sequence and allows you to choose which annotations to include in your sequence.
Get Started:
Quickly access recent files and folders using the new Get Started pane, or learn more about how to use SnapGene with links to short video tutorials, user guide articles, and the SnapGene Academy.
Search for and Import Sequences from Dotmatics Bioregister:
Quickly and easily search for sequences in Dotmatics Bioregister directly from within SnapGene based on the sequence name, Bioregister ID, or a similar sequence (BLAST search). Save a sequence of interest locally or open it in SnapGene right away. This integration requires Bioregister 6.1.0 or later.

New in SnapGene 6.2.2 (Apr 12, 2023)

New in SnapGene 6.2.1 (Apr 12, 2023)

New in SnapGene 6.2.0 (Dec 8, 2022)

New Functionality:
Suboptimal RNA secondary structures
RNA structures can be recalculated using adjusted Tm and other settings
Display and make sequence selections in Structure view
Coordinates and 5' / 3' end labels can optionally be displayed in Structure view
Added menu actions at the top right of Structure view to reset pane, rotation and scale
Added a ligation fidelity matrix to the Golden Gate Assembly tool for assessing overall reaction fidelity
Cut a Golden Gate Assembly vector with any enzyme (not just Type IIS enzymes)
Adjust overhangs for manually designed primers while simulating Golden Gate Assembly
Adjust the hybridization region for all PCR cloning simulations. When using automatic primer design, the hybridized region will be configured automatically, ensuring miscellaneous features are not transferred to the product when a 5’ primer extension by chance partially hybridizes to the template.
Copy or export the properties and amino acid data for full protein sequences or selected regions
Copy individual protein properties
Enhancements:
Check for and prevent simulating Golden Gate assembly if two adjacent fragments are set to be used directly and abutting ends both lack 5' terminal phosphates
Improved the appearance of many icons on low DPI displays
Display the selected MW in the selection bar for protein alignments
Improved the error message shown when attempting to ligate linear fragments that lack 5' terminal phosphates
Updated the Golden Gate Assembly dialog to include easy access to recommended enzymes
Improved the default sequence name when pasting FASTA encoded sequences into the New File dialog
Modernized application, file, and various other icons
Added links to NEBuilder® HiFi DNA Assembly and TOPO® Cloning tutorial videos.
Show complementary bases of neighboring overhangs in Golden Gate cloning mini-overviews
Zoom to fit by default when viewing RNA secondary structures
Fixes:
Fixed an issue where quality of sequences aligned to a reference was sometimes not shown when requested
Improved the appearance of tab controls on macOS
Improved the appearance of slider controls on macOS and fixed an issue that prevented vertically scaling peaks for traces aligned to a reference sequence
Improved overall stability
Fixed an issue that prevented simulating Golden Gate cloning when a golden gate site blocked by methylation was present within the insert or in the assembled product
Corrected an issue where when exporting translated features that use a custom genetic code (e.g. Amber) to GenBank the /transl_table qualifier should be omitted and this information is encoded using a /note qualifier instead
Fixed issues with importing multi-sequence GenBank files that contain empty sequences (name only)
Fixed an issue where protein sequences were sometimes imported from NCBI as DNA or RNA when using the import extra features option
Fixed issues with selecting the codons just upstream and downstream of the site of ribosomal slippage
Fixed an issue that sometimes prevented aligning bases adjacent to internal mismatching regions
Ensure "Show History" is always a blue clickable link in textual representation of History view
Corrected the default methylation for newly created sequences to match the default strain specified in Preferences
Disabled the 3-Letter Amino Acids action in the sequence view context menu when using compact mode
Fixed a crash when detecting common features
Fixed an issue where quality data was sometimes not shown for all sequences aligned to a reference
Fixed an issue with stripping out some formatting when copy and pasting from web pages into the description panel or other rich text controls
Corrected an issue where feature colors were not accurately shown when using dark mode
Addressed a number of issues with creating features in protein sequences
Only allow a single copy of the alignment dialogs to be shown at a time
Fixed the horizontal alignment of the "Show as Uninterrupted Circle" button in the side toolbar
Do not show a cursor when clicking and holding on a codon in Sequence view
Avoid showing duplicate copies of open documents from the Window menu
Do not show a translation window when starting SnapGene on a computer configured to use a non-English locale such as German but one that the application is not translated into
Removed duplicate "site" feature type from the feature type cascading menu
Improve area printed when printing RNA structures
Fixed an issue where printed RNA structures were sometimes blurry
Fixed an issue where an I-beam cursor was shown when mousing over Sequence view in contexts where arbitrary selections cannot be made such as the Silent Mutagenesis dialog
Fixed an issue that prevented detecting the preferred language on macOS
Fixed an issue where the wrong number of binding sites was sometimes listed in cloning dilaogs when simplified binding sites were shown
Fixed an issue where primers designed automatically and those specified manually were not always shown annealing to the template in the same manner
Fixed various issues when using multiple screens.
Various textual corrections
Fixed a stability issue when attempting to use a linear fragment directly when simulating Overlap Extension PCR
Fixed an issue where the application would freeze when attempting to generate primers for Golden Gate cloning if the fragments already contained one or more sites for the Golden Gate enzyme.
Fixed issues where windows were not always shown on the logical display when using multiple displays on macOS.
Improved opening older Geneious files.
Fixed an issue where alternate transcripts (isoforms) were incorectly listed already in and thus not imported directly when importing features from another file.
Fixed an issue that could prevent batch importing features
Fixed an issue where when importing an enzyme list unknown entries were imported as AanI.
Fixed an issue where using the Choose Primers command would fail to design primers for linear vectors or fragments if you did not first make a selection. SnapGene now correctly designers primers to use the entire linear sequence.
Fixed a stability issue when changing the number of fragments to 1.
Fixed an issue where if the first or last fragment in Overalap Extension PCR was not amplified by PCR the forward and/or reverse primers for amplifying the assembled linear fragment were not configured automatically when using the Choose Primers command.
Fixed ordering from Vector Builder
Fixed the link for more information about fonts and printing on Windows
Improved rendering buttons and images when dragging windows between low and high resolution displays
Fixed various memory leaks
Fixed an issue where primers binding sites with melting temperatures less than 30 C were not identified
Improved the behavior of the Secondary Structure zoom control
Improved decoding feature types from Vector NTI databases
Removed the MAFFT penalty shift setting since it was problematic
Updated links to the user guide and user guide articles

New in SnapGene 6.1.2 (Oct 12, 2022)

New in SnapGene 6.1.1 (Aug 18, 2022)

New in SnapGene 6.1.0 (Jul 6, 2022)

New in SnapGene 6.0.6 (Jun 24, 2022)

New in SnapGene 6.0.4 (May 4, 2022)

New in SnapGene 6.0.3 (Apr 18, 2022)

Enhancements:
impoved formatting when using the Copy Selected Primers and Export Primer Data commands.
(Requested by Di Xia)
Improved responsiveness of cloning dialogs when switching tabs and flipping fragments.
Improved responsiveness when making selections in multiple sequence alignments.
Improved responsiveness when performing or opening a file with an alignment to a reference sequence.
Fixes:
Fixed an issue with renaming folders in collections.
(Reported by Dinesh Babu Paudel)
Avoid switching from Map to Sequence view after importing sequences to align to the reference.
(Reported by Cary Valley and Michal Poborsky)
Fixed an regression where features in replaced regions were erronously retained during restriction cloning if the insert was the same size.
(Reported by Martha and James Smart)
Fixed an issue with decoding features from GenBank files generated by CHOPCHOP.
(Reported by Reuben Philip)
Fixed aligning sequences in a multi-sequence FASTA file with a reference.
(Reported by Fang Suo, Louise La Barbera Kastberg, Guttorm Haraldsen, and Ryan McNulty )
Fixed an issue with opening supported file types in Miscellaneous Files when viewing a collection.
(Reported by Dinesh Babu Paudel)
Fixed a default file name and extension when saving a sequence trace.
(Reported by Dinesh Babu Paude)
Addressed an issue where Sharepoint index conflict files resulted in new file notifications when working with collections.
(Reported by Andras Solt)
Improved stability when detecting common features.
Fixed an issue where the selection bar was blank after making a feature in a multiple sequence alignment.
Fixed a crash when attempting to create a custom feature type in SnapGene Viewer.
Fixed an issue that prevented loading non-installed custom feature types that are embedded within a file.
Improved stability with multiple sequence alignments.
Fixed a memory leak when creating, editing, or duplicating features.
Corrected an issue with history colors after performing PCR using primers that extend beyond the end of a linear template.
Fixed an issue with making RNA sequences from selections in large genomic sequences.
Fixed an issue where unnecessary menus were sometimes shown on the launch dialog.
Fixed various issues where characters right of a period in a agarose gel sequence name was not shown in the fragment list or source control
Removed unecessary message indicating upgrading to SnapGene is required to perform an alignemnt if one or more aligned sequences and an associated alignment to the reference sequence is already computed.
Improved overall stability
Addressed various memory leaks.

New in SnapGene 6.0.2 (Jan 14, 2022)

New in SnapGene 6.0.1 (Jan 12, 2022)

New in SnapGene 6.0.0 (Nov 30, 2021)

New Functionality:
Added a tool for adding enzymes sites to a coding sequence by silent mutation
Added a tool for removing an enzyme site from a coding sequence by silent mutation
Added support for custom features types not included in the standard set of GenBank feature types
Enabled changing the default color of standard Genbank feature types
Added support for saving and loading Agarose gel simulations as .gel files
Added support for features within pairwise alignments
Enabled adding, editing and deleting features in alignments
Added a features table when viewing pairwise and multiple sequence alignments
Enabled searching an alignment to find features
Enhanced Gibson, InFusion and NEBuilder HiFi Assembly simulation tools to allow the vector to be flipped
Enhanced cloning simulation tools to support adding, removing and re-ordering sequences
Included controls to filter the set of chosen enzymes based on the number of times and relative location an enzyme cleaves with respect to its recognition sequence
Enabled setting a default Codon Usage Table
Added tool for converting ng/uL to nM in the DNA Calculations dialog
Added base counts to the DNA Calculations dialog
Enhancements:
Enhanced the 'Blocks of 3' Sequence view format to enable aligning nucleotide triplets with the reading frame
Support for optionally displaying sequence names alongside the sequences when printing pairwise and multiple sequence alignments
Switched from "?" to "X/Xaa" in translations to represent ambiguous amino acids
Added Tm for the selected region in ssDNA sequences
Added a locking mechanism which sets files as read only to other instances of SnapGene when being edited. Note that the locking mechanism is not available on large files, and has short delay, so is not effective when files are opened simultaneously
Convert Psi to U when importing or creating a new RNA sequence
Added support for including binding site locations when exporting primer data
Added Gateway Cloning destination vectors pEXP3-DEST and pEXP4-DEST, and updated cross-references in descriptions for pEXP-DEST Vectors
Features and custom numbering are now retained when copying and pasting into the New Protein File dialog, or inserting or replacing residues in a protein sequence
Added support for pasting copied complementary primer pairs to configure an Agarose Gel lane
Improved explanation for how to change sequence methylation when an enzyme is blocked during Restriction Cloning
Added support for adjusting the resolution (ppi) and creating a transparent image when exporting maps from the command line interface
Included various textual enhancements
Fixes:
Included Nicking enzymes in the 6+ Cutters enzyme set
Remove secondary recognition sequence for TaqII as this does not result in cleavage
Restore last shown enzyme variant when returning to a previously viewed enzyme in the Restriction Enzymes window.
Reduced file size and sped up loading files by omitting features in History view for large ancestral sequences
Added support for the following non-standard qualifiers for all translatable feature types: calculated_mol_wt, codon, codon_start, exception, protein_id, transl_except, transl_table, translation
Non-standard qualifiers are now retained when importing and exporting (previously they were converted to /note)
Added support for /transl_table and /codon_start qualifiers with CDS features in protein sequences
Fixed an occasional issue on macOS where an empty SnapGene window appears which cannot be closed except by restarting SnapGene
Disabled subsidiary check boxes when appropriate in Preferences
Corrected mouse-over effects for Site features with multiple segments
Fixed an issue that prevented setting a protein point feature type to misc_feature, unsure, or variation.
Automatically change feature color when changing the type when adding a point feature if the color has not been manually adjusted.
Fixed an issue where U's were not converted to T's if either end of a linear DNA sequence is modified to be covalently closed.
Fixed an issue where unsaved files added to the align sequence tools were listed using the wrong name
Fixed an issue that sometimes prevented run-on translations from being shown in alignments
Ensured it is always possible to scroll to the last base in DNA files
Removed inappropriate methylation message which was shown when opening the features tab for some protein files
Corrected an issue that prevented pliancy from being shown when using the "Choose Alternative Codons" tool
Corrected various display issues when switching a lane in an agarose gel simulation to using a MW marker
Fixed an issue that prevented point features from being added to protein sequences
Require a product name to be specified when using the Mutagenesis tool
Ensured bases are always visible when history colors are shown
Always show shared codons in adjacent translated features within Sequence view
Fixed Align to Reference DNA sequence so that undoing sequences edits no longer hides the aligned sequences
Reliably display ORF's that wrap around the numerical origin in circular sequences
Fixed an issue that prevented some keyboard shortcuts from working while the launch dialog was visible on Linux
Correctly show the Description Panel by default when this preference is toggled on
Ensured the navigation buttons in the Choose Alternative Codons tool are properly enabled
Corrected an issue with searching for features in protein sequences when Region features are not shown
Fixed an issue where qualifier selections in Features view were lost when switching tabs
Fixed an issue where using undo while viewing an alignment to a reference sequence resulted in expanded aligned sequences being collapsed.
Fixed issues with Make Protein and Copy Translation with two abutting in-frame translated Features for which a codon spans the feature boundaries
Fixed lagging selection of checkboxes on windows when importing primers
Enabled jumping to next/previous regions across the origin using "Next/Previous Aligned Region" buttons
Clarified dialogs to indicate Java 8 is supported for Vector NTI Express database import
Fixed the default folder in Preferences > Files for opening being ignored by Open Files
Corrected an issue that resulted in primer names not being included in default document name when creating a new file from a primer pair selection
Fixed an issue that prevented using the NEBuilder tool with primers that are separated by less than 50 bp
Corrected an issue with refreshing the list of sequences after clearing the search control when using the Import SnapGene Online Sequences tool
Fixed an issue that prevented using preexisting non-overlapping PCR primers for the vector when using the NEBuilder tool
Corrected an issue that prevented dragging and dropping files onto Agarose Gel windows
Corrected an issue that prevented shown chosen enzymes when switching between documents in a collection
Removed unnecessary horizontal lines that remained after removing references in the Edit References window
Improved default size of the Edit References window
Corrected an issue with displaying the selection length for selections with sticky overhangs
Improved stability when making selections in sequences aligned to a reference
Removed ambiguous codons when using the Insert Codon and Choose Alternative Codons tools
Improved stability when using Opt-click to close all files
Improved overall stability and corrected various memory leaks
Restore selected history operation and display of history colors after undoing hiding an operation.
Corrected an issue where an erroneous message was shown indicating a purchase was required before installing an available software update.
Improved the name and icon shown for alignment documents in Window menus
Fixed an issue that prevented correctly displaying where sequences align to a reference sequence in Map view.
(Reported by Lauri Lintott)
Improved the appearance of simulated agarose gels on screen and when exporting to a file
Improved stability when saving multiple files in a collection
Improved the appearance of site features in linear maps when printing and copying to the clipboard.
Ignore collection index conflict flies created by OneDrive.
(Reported by Andras Solt)
Fixed an issue that prevented using selected primers to pre-populate controls in PCR-driven cloning dialogs.
Fixed position where the add/edit/duplicate protein feature dialogs appear
Improved stability when clicking on Save to Main Collection without a file selected
Correctly display the sequence name above enzyme sets that are associated with a single sequence in the side toolbar menu
Stability fixes when using splice to remove intros and new file from selection
Fixed wrong shortcut showing on Windows in search type combo box for search bar (Meta→Alt)
(Reported by Michael Lynge Nielsen)

New in SnapGene 5.3.2 (Jul 7, 2021)

Fixes:
Corrected an issue with showing aligned sequences as double-stranded DNA. (Reported by Christine Chidester, Lauren Flynn, and Clifford Dustin Rubinstein)
Addressed an issue with folders in collections stored on network drives. (Reported by Stefan Kalies)
Addressed a stability issue with viewing some primers in Sequence view. (Reported by Ferdinand Greiss)
Ensured correct reporting of the number of matches when searching ssDNA sequences. (Reported by Jeff Sekelsky)
Fixed a regression that prevented the display of some primer binding sites when simplified hybridizations are being shown. (Reported by Katjusa Brejc)
Increased the number of primer binding sites that can be shown in Map view. (Requested by Jadyn Cox, Hsinho Huang, and Sara Smith)
Fixed an issue that sometimes prevented showing the first aligned sequence when printing an alignment to a reference sequence. (Reported by Daiki Matsuda)
Corrected an issue with saving aligned reads to an ssDNA sequence. (Reported by Daiki Matsuda)
Improved stability when expanding sequences aligned to a reference DNA sequence. (Reported by Scott Brown)
Improved stability when choosing alternative codons.
Ensured that opened documents are always added to the recent files list.
Fixed an issue that could prevent enzymes from being displayed in older documents in collections.
Ensured that display options are always preserved when duplicating collection documents in a new window.
Removed a blank cascading menu that could appear in the Edit menu when using "Save As".
Improved stability when dragging trimming handles.
Improved stability when using Opt-click to invoke "Close All Open Files" on macOS.
Improved the appearance of the focus ring for comboboxes on macOS.
Improved the mnemonic shortcut for deleting a restriction fragment on Windows.
Improved the default filename when exporting an alignment.
Improved colors in cloning overviews.
Made various textual corrections.
Prevented unnecessary scrolling when undoing sequence modifications.
Improved stability when using short sequences aligned to a reference DNA sequence.
Improved stability when using "Splice to Remove Introns".

New in SnapGene 5.3.1 (Jun 9, 2021)

Fixes:
Ensured retention of unchanged alignment name and omission of name controls when using the "Replace" option when redoing an alignment.
Fixed an issue where File → Save did not work after redoing an unsaved alignment.
Preserved the display of preferred codons when switching between DNA and mRNA formats when viewing a codon usage table.
Allocated sufficient space to display the "Size" column in Features view when viewing ssDNA and ssRNA sequences.
Prohibited pasting when multiple files are selected in a collection.
Prevented a crash that would occur after double-clicking when importing SnapGene and Addgene online sequences.
Completely removed the installation folder when uninstalling on Windows.
Enabled "File → Export → Alignment..." and "File → Export → Consensus..." when viewing an alignment.
Made significant stability improvements.
Reduced memory usage.
Improved date formatting on Windows.
Improved button placement in History view.
Fixed an issue that could cause custom common features to be corrupted by using the right-click context menu to edit a common feature.
(Reported by several users)
Removed the "Hybridization Parameters" menu action when viewing an RNA sequence in a collection.
Improved manual adjustment of vertical scaling of sequences traces aligned to a reference sequence.
Fixed an issue that prevented importing from Vector NTI databases on Windows.
(Reported by Dunhua Zhang)
Addressed an issue with importing some Vector NTI Express databases.
(Reported by Max Fu)
Fixed an issue in which the text representation of History view did not always refresh immediately when edits were made or undone.
Ensured correct enabling and disabling of the "Edit History" control in History view when the history is modified.
Corrected an issue that allowed duplicate primers with the same name but different sequence case to be imported into a file.
Corrected various issues that could occur when attempting to add features to the common features database, or importing such features, if they were marked as not visible in the original document.
Ensured correct export of common features to the specified folder.
Addressed issues that prevented collections stored on Windows network shares from being listed as recent collections in the File → Open Collection menu.
Improved fonts and text placement in History view.
Improved the message shown if an alignment is selected in a collection.
Corrected an issue that could cause pop-up menus to remain open when the Launch dialog was closed.
Corrected an issue that prevented saving a new file created from a selection from being saved to an open collection.
Ensured remembering of a preference for showing additional binding sites that do not match at the 3' end.
(Reported by Dan Piraner)
Corrected a regression that prevented imported primers from being restricted to those that have a unique binding site.
(Reported by Lauri Lintott, Michal Dolezal, and Jadyn Cox)
Ensured that the chosen enzyme set and enzyme visibility are retained when undoing sequence edits.
(Reported by Scott James)
Ensured that bold is correctly used to highlight unique cutters after undoing sequence edits.
Reduced the file size when exporting maps and history as PNG images.
(Reported by Xavier Danthinne)
Improved the toggling of enzyme visibility when repeatedly clicking check boxes in Enzymes view.
Fixed an issue that prevented looking up an enzyme by right-clicking in the Enzyme or Sites column in Enzymes view.
Fixed an issue that incorrectly suggested a sequence trace has unsaved edits after using File → Save As.

New in SnapGene 5.3.0 (May 13, 2021)

New Functionality:
Added support for viewing features in multiple sequence alignments.
Enhanced History view with a Text format tab, and with an option to show the entire history.
Added support for RNA sequences as .rna files.
Enabled viewing files of all types simultaneously in a Collection using a new "All Files" area.
Enabled gaps to be displayed every 10th base for protein sequences, and every 10th or 3rd base for nucleotide sequences.
Added support for filling in DNA ends of annealed oligos to create a double-stranded DNA sequence.
Added support for annotating primers that anneal at the 5’ end but not the 3’ end.
Enabled viewing and printing chromatogram files in a wrapped multi-line format.
Improved the conversion of .geneious nucleotide and protein sequences and alignments.
Added DNA Ladders from Ecogen, TIANGEN, and Vazyme.
Enhancements:
Extended the range for the minimum required 3' match for primers from 25 to 35 bases.
Enabled export of alignments to rich text format .rtf files.
Enhanced the visualization of mutagenesis simulations and mutagenic primers.
Enhanced the response to mousing over a primer so that the binding site is now highlighted in gray.
Added support for /protein_id qualifiers for mat_peptide features.
Enabled printing to PDF on macOS when no printers are installed.
Added an indicator in the selection bar to show "DNA" or "RNA" as the sequence type.
Enhanced enzyme, feature, and primer label layout in Map view for linear sequences.
Added clickable "contact support" links to messages that pop up in various places.
Made terminator features directional in the common features database.
Added the keyboard shortcuts Cmd+1 / Cmd+2 / Cmd+3 for switching between tabs in chromatogram windows.
Enhanced cursor placement, highlighting, and trace data tooltips when the mouse cursor is between bases.
Changed the "Replace" button label in Collections to "Bulk Edit" for improved clarity and accuracy.
Improved primer binding sites to avoid bulges if a 5' N tail is present in the primer sequence.
Updated the MAFFT aligner to version 7.471.
Updated the Parasail aligner to version 2.4.2.
Added a shortcut (Shift + Spacebar) for scrolling one page up in multiple sequence alignments.
Streamlined toolbar on macOS.
Fixes:
Rationalized the View menu to show options relevant to the file type.
Removed the "Browse..." menu action that had no effect in the "Import Primers from a SnapGene File" dialog.
Adjusted the tooltips for buttons in the "Find" bar to make them more consistent with other tooltips.
Changed the heading in the Collection search dialog for Protein Files to say "Names" rather than "Names & Numbers".
Ensured that only a single /mod_base qualifier is allowed for modified_base features.
Added a ruler for protein sequences when viewing in compact format.
Fixed a bug with selection of the last item in Features, Primers, and Enzymes views.
Implemented immediate update of the version listed on the account administrator page after SnapGene is updated.
Corrected a regression in which sequence selection was lost after clicking in the Description Panel.
Corrected a regression with enzyme site selection in Lines mode of Enzymes view.
Ensured consistent display of the selection when switching to Sequence view.
Fixed an issue in which spaces were not shown after commas on macOS Big Sur.
Fixed a non-functional "Choose Enzymes..." command in the "Choose enzyme set" dropdown menu.
Corrected a regression that caused overtyping of characters in the primer name fields of the Simulate Agarose Gel dialog.
Ensured correct refreshing of primer binding sites when changing hybridization parameters.
Prevented truncation of 3' overhangs that extend beyond the end of a circular sequence.
Prevented input of an invalid location in the Go To dialog for sequences aligned to a reference DNA sequence.
Fixed some tabs that displayed as white text on a white background on macOS Big Sur.
Ensured that features are not lost from inserts in cloning operations when windows are opened or closed.
Corrected the color of the gray bar below the list box in the Collection interface.
Prevented "< Please choose >" from being propagated from the Anneal Oligos dialog to the oligo names in the resulting history.
Ensured that in the Anneal Oligos dialog, a double-click on a compatible enzyme is needed to transfer focus to the Restriction Enzymes dialog.
Configured the pull-down menus in the Anneal Oligos dialog to refresh when documents are opened or closed.
Ensured that the specified font size is used when printing the Description Panel.
Fixed an issue with the folder location used when exporting standard common features.
Improved scrolling performance in Enzymes view.
Fixed the default file name chosen when exporting a single file from a Collection.
Improved the reliability of displaying the warning in the Print dialog on Windows about printing to PDF.
Ensured that tabbed window controls on macOS are reliably shown.
Improved the background color display in Map view.
Fixed issue in which keywords could be used as the construct name for some GenBank/GenPept files.
Improved the opening of SeqBuilder files.
Addressed issues with importing references from another file.
Improved the quality when exporting maps at high resolutions.
Updated Map, Sequence, and other views when protein sequences are zoomed.
Implemented hiding of zoom controls in a collection when switching from a long sequence that supports zooming to a shorter one that does not.
Prevented unnecessary display of a message about unsupported qualifiers during NCBI import when the content includes nonstandard qualifiers (e.g., /UniProtKB_evidence) that are deliberately converted to /note qualifiers.
Corrected an issue in which some line breaks in /note qualifiers were not preserved when opening GenBank or GenPept files.
Addressed a potential stability issue when viewing protein files.
Fixed copying of maps and histories on macOS, and improved the quality when pasting such content into applications such as Microsoft Word or PowerPoint on macOS.
Improved the message shown when attempting to use a sequence over 1 Mbp to compute a pairwise alignment.
Ensured correct identification of macOS Big Sur when sending anonymous user statistics.
Ensured correct display of a trace file icon in the Windows menu.
Fixed various issues with specifying and displaying the /collection_date qualifier.
Addressed an issue that could result in sequence characters moving slightly after periods of no mouse activity on Windows and Linux.
Simplified the choice of a destination folder during import into a collection by making the "Add" button the default.
Improved the display of feature names on Windows during pliancy and selection.
Fixed the Redo shortcut on Linux.
Improved margins and alignment in various windows and dialogs.
Improved the default placement of a window created via File → Open when no document was previously open.
Improved stability while viewing collections.
Avoided duplication of DNA documents in the Window menu after converting to single- or double-stranded format.
Corrected the shortcut for Overlap Extension PCR of two fragments.
Ensured that if the side toolbar button is used to show alignments and there are no currently aligned sequences, the software asks which files to import to align to the reference sequence.
Corrected an issue in which unmodified alignment documents sometimes indicated unsaved changes.
Corrected issues with dragging collection files onto other applications.
Fixed a crash when saving an alignment to a collection.
Disabled "Actions → Convert to Single-Stranded..." when viewing alignments.
Corrected an issue that prevented conversion of a feature translation to upper- or lowercase if the last selected codon was located at the end of the sequence.
Fixed a bug in which an open document might not be listed in the Window menu or in the lists of open documents in cloning dialogs, while the launch dialog would remain visible.
Fixed an issue that could result in two copies of the application running on macOS.
Ensured correct rendering of multi-region Site features that span multiple rows in Sequence view.
Addressed a stability issue when exporting and opening the alignment consensus.
Removed the dead "Browse..." action in the source menu when importing features from BED, GFF3, or GTF files.
Ensured that "Primers → Sort Primer List..." executes the desired sort.
Updated outdated web links to online resources.
Ensured correct residue numbering for Smith-Waterman (local) pairwise alignments.

New in SnapGene 5.2.5 (Apr 27, 2021)

New in SnapGene 5.2.4 (Dec 15, 2020)

New Functionality:
Added DNA ladders from GeneBio Systems.
(Requested by Dan)
Fixes:
Improved application stability when dragging out selections.
(Reported by Kengo Adachi and others)
Corrected a regression to ensure detection of restriction sites whose recognition sequences span the numerical origin.
(Reported by Anthony Picard)
Populate the "Description" fields when pasting GenBank content into the New File dialogs.
(Reported by Dustin Rubinstein)
Improved the detection of sequence type when importing DNASTAR SeqBuilder files.
(Reported by Oleh Rymarenko)
Corrected a regression to restore transfer of primers when pasting a copied DNA sequence.
(Reported by Peter Diebold)
Fixed an issue that could result in editing-induced disappearance of a sequence aligned to a reference DNA sequence.
(Reported by Paula)
Enabled simulation of Gateway BP and LR recombination around the numerical origin.
(Reported by Matthew Sale)
Improved application stability when searching for enzymes, features, and primers.
Corrected a misleading message that was shown when a problem occurred during program activation.
Ensured that the enzyme set indicator does not occlude content after scrolling to the bottom of Sequence view.
Streamlined the side toolbar in the Insert Codons, Choose Alternative Codons, Browse Common Features and Insert Feature dialogs.
Restored highlighting of the called base under the mouse when viewing sequence traces.
Improved application stability when using the "Find similar DNA sequences" command.
Improved performance when showing the Add Primer dialog and other dialogs that provide controls for choosing files.
Ensured highlighting of the inserted region for Gateway BP cloning in the Insert tab, and of the ancestral insert in History view for the resulting product file.
Restored import of ssRNA sequences as double-stranded rather than single-stranded DNA.
Prevented repetitive alignment to a reference sequence when making simple edits such as insertions, deletions, and same-size replacements.
Ensured that the Next button is the default control after searching a sequence trace.
Ensured correct scrolling of Sequence, Features, and Primers views in response to a change in the selection, but only when appropriate.
Improved application stability when quitting.
Improved application stability when hovering over aligned sequences.
Improved application stability when mousing over features.
Improved application tability when searching a collection for a named feature.
Improved application stability when importing primers.
Improved reliability when importing from NCBI.

New in SnapGene 5.2.3 (Nov 23, 2020)

Corrected a regression to enable the "Copy" command when a portion of an aligned sequence is selected.
(Reportd by Jai Padmakumar)
Corrected an issue that could prevent protein search results from being shown.
(Reported by Renato Lemgruber)
Improved the size and placement of the License Agreement and Align Multiple Sequences windows.
(Reported by Brian Tooker)
Ensured proper opening of GenBank files that omit the molecule type in the LOCUS line.
(Reported by Oliver Coleman)
Fixed an issue that could prevent using a attR Gateway site that lacks an optional leading nucleic acid.
(Reported by Robert Bill)
Fixed an issue with using Gateway fragments whose junctions lie at or very near the numerical origin.
(Reported by Robert Bill)
Ensured that files and collections located on network drives are included in the Open Recent File and Open Collection menus.
(Reported by Katherina Witte)
Fixed various glitches with displaying codon and ORF selections in Sequence view.
(Reported by James Scott)
Improved the appearance of tabs on macOS 11 Big Sur.
Corrected a regression to ensure auto-scrolling in Sequence view for selections made using the minimap or another view.
(Reported by Stuart Cahalan, Scott James, and Théo Grebert)
Corrected a regression to ensure display of restriction sites in sequences aligned to a reference DNA sequence.
Fixed an issue that resulted in ORFs sometimes not being shown.
Ensured that "Find" matches remain highlighted after switching away from and then back to Sequence view or Map view.
Ensured that "Find" matches are shown after restoring the "Find similar DNA sequences" controls.
Ensured that palindromic "Find" matches are highlighted in both strands.
Ensured proper display of "Find similar DNA sequences" matches that wrap around the numerical origin.
Improved the behavior of the search box in the Choose Enzymes window when searching for a noncutter while the "Hide noncutters" checkbox is checked.
Fixed an issue with detecting Gateway sites that have been customized by the user.
Fixed an issue with annotating Gateway sites that lie near the numerical origin after performing BP or LR cloning.
Ensured reliable import of features from SwissProt files.
Ensured reliable opening of SwissProt files that contain limited header information.
Corrected a regression to force use of the correct font in the New DNA File and New Protein File dialogs.
Ensured accurate display of multiple sequence alignment file names in the Window menu on Linux.
Improved reliability when installing software updates on macOS Big Sur.

New in SnapGene 5.2.2 (Nov 6, 2020)

New in SnapGene 5.2.1 (Oct 30, 2020)

New in SnapGene 5.2.0 (Oct 13, 2020)

New in SnapGene 5.1.7 (Sep 22, 2020)

New in SnapGene 5.1.6 (Sep 16, 2020)

New Functionality:
Added Agilent TapeStation ladders.
(Requested by Gavin Johnson)
Fixes:
Corrected a regression that prevented decoding of features in Gene Construction Kit files.
(Reported by Matthew Mulvey and others)
Corrected a regression that prevented the bacterial transformation strain from being applied to the cloning product.
(Reported by Kengo Adachi)
Fixed an issue with applying the "Limit file history" preference.
(Reported by Michael Taschner)
Improved detection of Gateway attR1, attR2 and attR4 sites.
(Inspired by Mily Ron)
Improved the default binding site shown when invoking the Edit Primer dialog for a primer with multiple binding sites.
(Reported by Karim Hyder)
Corrected an issue with simulating Gateway cloning using att sites that lie across the numerical origin.
(Reported by Dominic Esposito)
Removed an outdated comment regarding PmlI losing activity when stored at -20°C.
(Reported by Wael Tadros)
Corrected the Import Primers dialog to proceed when Enter/Return is pressed.
(Reported by Stuart Cahalan)
Fixed an issue that could result in peak data disappearing when editing Sanger sequence traces.
(Reported by Dale Cowley)
Corrected a regression that prevented Shift-selecting a range of primers in Primers view.
(Reported by Dan Kraut)
Removed the "Fixed Line Width" button from the side toolbar in the Anneal Oligos dialog.
Corrected various stability issues when using cloning dialogs.
Ensured that the Sequence view minimap is consistently shown.
Fixed an issue with migrating the chosen enzymes when cloning while using a custom local enzyme set.
Corrected a regression that could cause the Browse Common Features dialog to switch from Sequence to Map view when the displayed feature was changed.
Improved the tooltips for history operations.
Ensured that changing the sequence methylation reliably updates the methylation state in the Description Panel.
Improved the document icon for DNA alignments to include a shadow.
Corrected an issue with splitting the view after having previously done so.
Corrected an issue with using Shift and the Left/Right arrow keys to move selected ranges across an entire gap in an alignment.

New in SnapGene 5.1.5 (Jul 20, 2020)

New Functionality:
Added a "Copy Rich Text" command for selections in alignments, to provide the option of copying either simple sequences or sequences with metadata.
Enhancements:
Added Invitrogen's "pScreen-iT LacZ-Dest" to the list of Gateway® Destination vectors.
Modified the statistics in pairwise alignments to show two digits after the decimal point instead of one.
Added time estimates to various progress dialogs.
Improved the order of "Copy" actions in the Edit menu.
Made various textual, alignment, and spacing improvements.
Enabled export of a map or history while viewing any tab.
Fixes:
Ensured reliable import of primers copied to the clipboard using Microsoft Office.
Added support for dragging and dropping FASTA archives into the Assemble Contigs dialog.
Preserved zoom and split view display options when switching between files in a collection.
Enhanced the Gene Construction Kit importer to capture the full set of notes in the "General Info" section.
Improved stability when computing and viewing multiple sequence alignments.
Corrected an issue that could cause features to be erroneously detected around the numerical origin of a linear sequence.
Ensured that proper file extensions were included when batch converting files from one format to another.
Ensured correct setting of the default button in the Find controls when pressing and releasing Shift in a sequence trace window.
Corrected a regression with the navigation buttons when viewing an alignment to a reference sequence.
Addressed issues with the purple bar and the Tm column when importing primers from another file.
Corrected the displayed molecular weight when adding a translated feature to the common features database.
Removed the colors button in cloning dialogs, and streamlined the side toolbar in the Edit DNA Ends, Browse Common Features, and Mutageneis dialogs.
Improved the display of long sequence names within circular maps.
Corrected a regression by removing cut locations for ancestral restriction sites in History view.
Removed the inappropriate "Preserve feature annotations" control from the New File dialog, and the inappropriate "Detect common features" control when inserting or replacing bases in a sequence trace window.
Improved stability when assembling contigs using FASTQ data.
Disabled the Show/Hide All Enzymes commands when viewing protein files.
Corrected an issue in which the endpoints of a selection were not updated in the selection bar after renumbering the origin of a linear sequence.
Fixed an issue that prevented immediately using SnapGene without restarting after activating a Flexera-based shared license.
Corrected an issue with computing % GC when partially degenerate residues (B, D, H, and V) were present.
Ensured that only the zoomed region is shown for the root map in History view.
Addressed an issue in which the Save As dialog would vanish immediately when attempting to choose a different name instead of saving over an existing file.
Ensured that enzyme set menus are refreshed after using Manage Enzyme Sets.
Ensured that the desired endpoint modifications are correctly applied when designing a synthetic construct.
Improved the registration of file associations on macOS.

New in SnapGene 5.1.4.1 (Jul 20, 2020)

New in SnapGene 5.1.4 (Jun 17, 2020)

New in SnapGene 5.1.3 (May 21, 2020)

Enhancements:
Enhanced Sequence view so that when two panels of sequence are visible in a split window, the minimap at the top shows the visible regions from both panels.
Enhanced cloning dialogs to fit on smaller displays.
(Requested by Fayang Zhou)
Support polyA_site point features.
Made various textual enhancements.
Fixes:
Enhanced the GFF3 importer to handle files that mark a single sequence with multiple references.
(Reported by a customer)
Fixed an issue that prevented opening of some Vector NTI® .apr alignment files.
(Reported by K.L. Cheung)
Corrected a regression that prevented files in a collection's "Working Set" from being listed in source menus in action dialogs.
(Reported by Thom Hughes)
Improved stability when importing protein features from another SnapGene file.
(Reported by Anton Schmitz)
Corrected an issue that could result in poor alignments.
(Jinyeong Cheon)
Corrected a regression that prevented restriction sites blocked by methylation from being shown in gray in Enzymes View using Numbers mode.
Corrected a regression that prevented sorting of restriction sites in Enzymes view by location of the first site or by distance from the selection.
Ensured proper import of SnapGene online sequence files that contain "&" in their names, such as the COVID-19 genome file.
Corrected a regression that could prevent enzymes in aligned sequences from reflecting the chosen option for displaying enzymes.
Ensured that Enzymes view does not scroll when toggling enzyme visibility.
Corrected an issue that made it difficult to trim aligned sequences by dragging a trimming handle when using double-stranded DNA format.
Improved the export to GenBank and other text formats of features that contain "&" and other symbols in qualifiers.
Improved the appearance of a selection in an aligned sequence when manual trimming partially occludes the selection.
Corrected a regression that prevented invoking the Destroy Restriction Site or Remove Restriction Fragment dialogs by pressing Delete or Backspace in Enzymes view.
Ensured that toggling enzyme visibility no longer marks a file as unsaved.
Fixed an issue that could prevent dashes within gaps from being shown when viewing an alignment to a reference DNA sequence.
Prevented aligned bases from being shown in red at the endpoints of an alignment.
Fixed an issue that could cause "Redo Alignment" to fail for some files.
Ensured that the Edit Feature dialog correctly indicates that segment ranges can overlap if features with overlapping segments were imported from GenBank or other file formats.
Improved the default ratio between the two panel heights when generating a split window.
Prevented unnecessary vertical space from being allocated when laying out aligned sequences in double-stranded DNA format when enzymes are visible.
Improved the file information shown for registered file types in the Windows Explorer and the macOS Finder.
Improved the display of aligned regions in Map view.

New in SnapGene 5.1.2 (May 9, 2020)

New in SnapGene 5.1.1 (May 6, 2020)

New in SnapGene 5.1.0 (Apr 15, 2020)

New Functionality:
Enabled DNA and protein sequence windows to be split to show two views, one above the other.
(Requested over the years by multiple users)
Added support in the Description Panel for various reference types including books, database entries, patents (which can be imported from online databases), theses, web links, and more.
Configured /citation qualifier values to link to specific references, which are accessible via tooltips and clickable links in Features view.
Added optional page number entries for /citation qualifiers.
Enabled enzyme visibility to be adjusted in Enzymes view using check boxes, mirroring the controls used for Features and Primers views.
Enabled flexible feature detection with an adjustable similarity threshold when importing features from another file.
Added support for exporting aligned sequence trace data using a tab-separated format.
(Requested by Yves Girerd-Chambaz)
Enabled BLAST for multiple selected sequence files in a collection.
(Requested by Charles Dozois)
Added a pre-defined enzyme set for Type IIS enzymes.
Enabled import of features or primers from another file, or detection of common features, for multiple selected DNA files in a collection.
(Requested by Michael Gotrik)
Enabled simultaneous flipping of multiple selected DNA sequences in a collection.
Added support for linking folders of the same name in different areas of a collection, with "Go to ..." shortcuts for switching between related folders in different areas.
(Requested by Mily Ron)
Enabled the "Make Protein" and "Reverse Translate" commands, when operating within a collection, to save the output files to a linked folder in a different area of the collection.
Added support for batch replacement of Description Panel fields for files in a collection.
(Requested by Samuel Tremblay-Belzile)
Added MW markers from Nacalai Tesque.
(Requested by Tomonori Hoshino)
Added MW markers from FroggaBio.
(Requested by Michael Ostrovski)
Added MW markers from Newmarket Scientific.
(Requested by Sabrina)
Added the remaining TrackIt™ MW markers from Thermo Fisher.
(Requested by Slava Gurevich)
Improved feature tooltips when using compact mode in Sequence view.
(Requested by Bandar)
Enhancements:
Reduced the height of linear maps by enabling items to be superimposed without sacrificing legibility.
(Requested by Vishal Chaudhari)
Changed the defaults to show HF® and FastDigest® information in the Restriction Enzymes dialog, while allowing these defaults to be adjusted.
(Requested by Silvana Jirka)
Enhanced the File > Export cascading menu to enable export of multiple files or a list of files from a collection.
(Requested by Gurumoorthy Krishnamoorthy)
Added support for a color attribute when importing features from GFF3 format.
(Requested by Matthew Kirk)
Added support for specifying the line break characters when exporting to text file formats.
(Requested by Tim Fallon and Tom Chappell)
Enabled long map labels to span two lines in circular Map view.
(Requested by Chun Cao)
Configured Sequence view to retain visibility of the scrolled region when toggling horizontal scrolling.
(Requested by Kengo Adachi)
Enhanced the flexibility of code number display in collection lists.
(Requested by Tim Nierhaus)
Added a keyboard shortcut for "Import UniProt Sequences".
(Requested by James Wright)
Enabled colors in multiple sequence alignments to be copied to the clipboard.
(Requested by Monir Ejemel)
Provided the option to differentiate "A" traces using a striped pattern for users with color vision disabilities.
Provided an adjustable similarity threshold for detecting common features.
Enabled the "Make Protein", "Reverse Translate", and "New File From Selection" commands to save the output files to the same collection.
Allowed the genetic code to be specified when converting a selection in a DNA alignment to a protein alignment.
Ensured that when sorting by Code Number or Alias in a collection, any files with blank entries are placed at the end of the list.
Converted SnapGene to a 64-bit application on Windows, thereby improving performance and stability.
Ensured that scrollbars are shown only when necessary in Map, Sequence, and History views.
Improved the wording in the Restriction Enzymes dialog to make it clearer when a supplier offers multiple variants of an enzyme.
Changed the License Agreement dialog so that it is no longer modal, and added support for printing or saving this document using keyboard shortcuts.
Made various textual, color, and icon enhancements.
Fixes:
Configured the Find control to show bottom strand results when using compact format in Sequence view.
(Requested by Bandar)
Prevented extra line breaks from appearing after export of some qualifier values to GenBank and EMBL formats.
(Reported by Karen Ross)
Ensured that all controls in alignment dialogs can be translated into Japanese or Chinese.
Ensured that collection folder names for selected items never appear in List view.
Enabled scrolling up using Shift + Spacebar in Sequence view.
Fixed paging up and down using Function + Up/Down keys, and scrolling to the start or end of the sequence using Function + Left/Right keys.
Ensured that ancestral blunt cutters can be shown in green in History view after import from Vector NTI® or other file formats.
Prevented unnecessarily asking to add methylation when specifying "Escherichia coli" as the Source for a Natural DNA sequence.
Corrected an error with internal array data when editing trace sequences.
Ensured that linearizing or circularizing a DNA sequence populates the Sequence Author field with the default author.
Configured Enzymes view to show enzyme sites in red upon mouseover in both the main view and the lower map.
Corrected codon frequencies for reverse directional ORFs.
Ensured that the Description Panel flows to the bottom of the window when zoom controls are shown.
Fixed various issues with importing primers into DNA files in a collection.
Ensured that the map label in a circular map never overlaps features.
Disable menu File > Export > History when no history exists in sequence file.
Fix Blasting selected primer in a collection file.
Fix Tools > Blast Selected Protein with a collection file.
Ensured that the Previous button in the Find controls is shown in blue only if the Shift key and no other key is pressed.
Adjusted the behavior for sequence traces so that mousing over an ambiguous base darkens the curves for multiple bases.
Prevented accented characters from being accidentally inserted into a DNA or protein sequence when holding down letter keys on macOS.
Improved the foreground color within features while using compact Sequence view.
Improved feature pliancy while using compact Sequence view.
Fixed an issue in which pressing the Shift key resulted in a button changing color in the "Import Features from a SnapGene File" and "Detect Common Features" dialogs.
Improved the look and feel of controls for Enzymes view on Windows.
Preserved formatting when creating hyperlinks.
Improved horizontal alignment of values shown in the Properties tab for protein sequences.
Enabled proper export of /citation qualifier values to GenBank, GenPept, and EMBL formats.
Ensured that suppliers remain selected after dragging them in the Enzymes tab of the Preferences dialog.
Updated the MW calculation for a full sequence in the DNA Calculations window after 5' phosphates are added or removed.
Enabled bottom strand matches to search queries in Sequence view when using compact mode.
Ensured that qualifier selections in Features view are cleared when selecting features or transferring focus to the Description Panel.
Configured a collection to show and select imported files even when those files are not in the currently chosen category.
Fixed an issue that could result in labels for Site features not being shown entirely within a protein sequence window.
Improved the horizontal placement of names and connecting lines for site features in Sequence view.
Fixed an issue in which selections in Features and Primers views sometimes Disabled controls for setting the DNA color when using either compact Sequence view or Map view with features on the DNA line.
Fixed issues with displaying enzymes that make two double-stranded cuts when a site is near the end of a linear sequence.
SNAP-6417 Copy Alignment Colors to Clipboard Requested by Monir Ejemel.
SNAP-6783 Import VNTI Express Designer Database Reported by Dave Karig.
SNAP-6785 Crash Importing VNTI Express Designer Enzyme Names Reported by Dave Karig.

New in SnapGene 5.0.8 (Mar 24, 2020)

Enhancements:
Added support for importing whole genome shotgun sequencing projects from NCBI.
(Requested by Chance Meers)
Added a sequence length indicator for sequences imported into the Assemble Contigs dialog.
Made various text, color, and icon enhancements.
Enabled "Save All", "Save to Collection", and "Save to Main Collection" commands when multiple files are selected in a collection.
Fixes:
Corrected an issue that could cause the font used in Sequence view to be wrong on Windows.
(Reported by Ben Mcneil, Anna Doyle, Terese Tansey, and Dominic Esposito)
Fixed an issue that prevented double-clicking from opening files with spaces in their names on Lubuntu Linux.
(Reported by Sahand Jamal Rahi)
Ensured that features that wrap around the numerical origin are always properly displayed.
(Reported by Théo Grebert)
Corrected an issue that prevented opening sequence traces from remote locations when the file path includes non-Latin characters.
(Reported by Yusuke Maeda)
Fixed a stability issue when expanding the "Aligned Sequences" menu using SnapGene Viewer.
(Reported by Venkat Kalyana Sundaram)
Ensured correct creation of features with annotated gaps from selected aligned sequences.
(Reported by Olaf Kranse)
Ensured that newly imported sequences for aligning to a reference DNA sequence are always trimmed properly.
(Reported by Ridvan Cetin)
Prevented a collection from becoming unresponsive when adding files manually before dismissing the "Add DNA File" dialog.
(Reported by Gage Leighto)
Fixed an issue with writing feature names to GenBank format for assembly_gap, mobile_element, propeptide, regulatory, and telomere feature types.
(Reported by Hassan Tarabai)
Ensured that release notes are consistently shown when announcing that a new version of SnapGene is available.
Fixed an issue that resulted in the End User License Agreement dialog being too tall on smaller displays.
Ensured that matches to searches are always shown.
Ensured that Shift-clicking items in a list consistently results in a range-based selection.
Fixed an issue that prevented aligning a pair of DNA or protein sequences on some Linux systems.
Improved the conversion of DNA alignments to protein alignments.
Improved the mouse cursor for various controls that show tooltips but do not respond to mouse presses.
Ensured proper display of the message indicating that hybridization parameters need to be adjusted to show primer binding sites.
Removed the "Show alignments" button from the side toolbar in the Design Synthetic Construct dialog.
Ensured correct labeling of protein feature segments after making a protein from a DNA feature that contains introns.
Changed "bases" to to "residues" in the REFERENCE field when exporting protein sequences to GenPept format.
Corrected an issue with annotating common features that are found at the beginning of the sequence.
Improved highlighting of feature boundaries under the mouse cursor when using compact format in Sequence view.
Fixed an issue that prevented import of unsaved open sequences into the "Assemble Contigs" dialog.
Corrected a stability issue that resulted from closing a window while a menu was expanded.
Corrected an issue with aligning multiple DNA sequences that were recently imported from NCBI.
Ensured that header buttons are not always aligned with the column content when viewing a collection in List format.
Improved the behavior when double-clicking folders in collections.
Ensured that appropriate icons are shown next to unsaved files in the Window menu.
Fixed an issue that could prevent operation of the MUSCLE aligner.
Ensured that the Print and Save buttons in the toolbar are always correctly enabled or disabled when viewing a collection.
Corrected an issue in which protein sequences that count from a value other than 1 were sometimes shifted to the right in Sequence view.
Improved the display of a cursor placed within a gap when viewing alignments to a reference DNA sequence in Sequence view.
Corrected an issue that could result in feature labels being shown without being connected by a stem.

New in SnapGene 5.0.7 (Dec 16, 2019)

Enhancements:
Updated the common features database.
Added a "Clear List" action to the bottom of the menu in the "Import Primers from a List" dialog.
(Requested by Michael Baughn)
Fixes:
Fixed a regression with the background color for copied and exported gels.
(Reported by Russ Collins)
Improved compatibility of collections that are stored on a Google Shared Drive.
(Reported by Kurt De Vos and Michael Gotrik)
Improved stability when importing Vector NTI databases.
(Reported by Christoph Harms)
Corrected an issue that could cause aligned sequences to disappear after saving.
(Reported by Denise Lanza and Adrian R)
Substantially improved the decoding of alignment and sequence trace data from Vector NTI .cep files.
(Reported by Dale Cowley)
Fixed an issue in which aligned copied sequences were not always shown.
(Reported by Leonid V)
Corrected a regression that could result in inferior alignments to a reference sequence.
(Reported by Elisabeth Boger)
Restored the "Import Features from a SnapGene File..." command to the Features menu when working with a protein file.
(Reported by Anton Schmitz)
Improved the import of feature name, color, and directionality data as well as the map label from GenBank files exported by Vector NTI.
(Reported by Terete Borras)
Adding missing Edit → Copy Amino Acids menu actions when viewing a protein file in a collection.
Streamlined the interface by not displaying feature descriptions when detecting common features or importing features.
Ensured that tapping Enter correctly selects the contents of line edit fields in the Description Panel.
Ensured that ambiguous bases in traces are consistently shown as black on a yellow background.
Disabled Undo after making an edit to a very long DNA sequence because such operations cannot presently be undone.
Fixed a regression that caused deletions at the very beginning of a sequence to generate unexpected results and to be especially slow in large sequences.
Prevented adding a folder with a duplicate name in a collection by disabling the "OK" button instead of showing a scary window.
Improved the display of hybridization for primers in the Mutagenesis dialog and PCR-based cloning dialogs.
Enabled mutagenesis to be simulated using a primer that hybridizes perfectly but includes degenerate bases.
Made various format improvements for printing.
Ensured that ruler tick marks are always the correct height in Sequence view.
Improved colors for protein feature labels and lines with dark and other nonstandard background colors.
Ensured that all trace data are shown near trimming handles for aligned sequences.
Fixed a regression that sometimes resulted in disappearing features and grayed-out bases when nonaligned regions were shown by dragging the right trimming handle.
Added a warning before attempting to align pairs of very large sequences.
Fixed various visual issues when viewing nonaligned ends in an alignment to a reference DNA sequence.
Improved scrolling to mismatches and to the next or previous aligned region in an alignment to a reference DNA sequence, and properly disabled these controls when there is no destination for scrolling.
Fixed setting the collection folder icon when creating a new collection or while asking to open the main collection.
Corrected an issue that could cause the wrong name to be shown for unsaved open files when setting the options for a pairwise alignment.

New in SnapGene 5.0.6 (Nov 25, 2019)

New in SnapGene 5.0.5 (Nov 15, 2019)

New in SnapGene 5.0 (Nov 15, 2019)

Version 5.0 adds new capabilities and display options including pairwise alignment, import from the Ensembl database, support for directional TOPO® cloning, and improved tools for alignment to a reference DNA sequence.
Pairwise Alignment:
Pairs of DNA or protein sequences can be analyzed by local, global, or semi-global alignment.
Import from Ensembl:
Gene or transcript data from the Ensembl genome browser can now be imported directly into SnapGene.
Directional TOPO Cloning:
A new interface simulates directional TOPO cloning into topoisomerase-activated vectors.
Flexible Alignment to a Reference:;
The interface for aligning to a reference DNA sequence has been enhanced. Controls for various display options are more intuitive, and alignment can be restricted to a designated strand or region of the reference sequence.
Draggable Nonaligned Ends:
For a sequence that has been partially aligned to a reference DNA sequence, the nonaligned end portions can now be dragged out and visualized.
Anza Enzymes:;
The Anza™ enzyme system from Thermo Fisher (Invitrogen) has been incorporated into SnapGene’s enzyme database.
Customizable Background Color:
The background color for the SnapGene interface can be changed.
Visibility Controls for Feature Types:;
Features can be shown or hidden based on feature type.
New Options for Amino Acids:
Amino acids in a translated feature can be set to lowercase, and a stretch of amino acids can be copied in 3-letter format.
Codon Frequencies Calculator:
A codon frequencies table can be generated for one or more translated features.
DNA-to-Protein Alignment Conversion:
A selected region of a DNA alignment can be translated to generate the corresponding protein alignment.
Intron Annotation for an Aligned cDNA:
When a cDNA is aligned to a reference genomic DNA sequence, the cDNA can be used to create a feature in which gaps are annotated as introns.
Extended Selection Endpoints in Maps:
Selections are now marked with extended lines, which clarify the selection endpoints and also enhance visibility for small selections.
Importer for DNASIS Files:
Files from the legacy DNASIS program are now recognized by SnapGene.

New in SnapGene 4.3.11 (Aug 14, 2019)

New in SnapGene 4.3.10 (Jun 15, 2019)

New in SnapGene 4.3.0 (Feb 6, 2019)

New Functionality
Added support for de novo contig assembly from overlapping sequences or Sanger sequence traces.
(Requested by multiple customers)
Added an option to create a sub-alignment by selecting and then realigning part of a multiple sequence alignment.
Preserved custom numbering of aligned sequences when computing multiple sequence alignments.
Added options to add an alignment using a different algorithm or to remove an existing alignment in a multiple sequence alignment window.
Provided support for nicking endonucleases.
(Requested by Luay Joudeh, Rufeng Wang, Sarah Darling, Ivan Mikaelian, John Kung, Dustin Rubinstein, Di Yu, and others)
Added the ability to remove a single-stranded region from a linear sequence by selecting from a DNA end to a nicking endonuclease site and pressing Delete.
Enabled deletion of a restriction fragment after selection from the end of a linear sequence to a restriction site.
Added support for point features, including import of point features from other file formats.
(Requested by Allan Drummond, Tyler Bradshaw, and Michele McConn)
Added the ability to highlight one or more enzyme sites.
(Requested by Dan Strongin and Brigitte Lavoie)
Added support for copying or exporting part or all of the consensus sequence from a multiple sequence alignment.
(Requested by Elaine Joseph, Emily Isgur, Casey Keyes, and Shannon Phan)
Improved the consensus format in multiple sequence alignments to use light gray X's or N's where consensus is lacking.
Enabled the import of copied and open sequences, as well as import from NCBI and UniProt, when computing multiple sequence alignments.
Enabled recomputing of an alignment to a reference DNA sequence using the "Aligned Sequences" button menu.
Configured manual trimming of sequences aligned to a reference DNA sequence to be both undoable and saved, and set the trimming stringency to be undoable and saved on a per-file basis.
(Requested by George Ghanim, Icon Genetics, Dave Bailey, Aaron Alt, Mily Ron, and Lennert Janssen)
Ensured that small edits to a sequence aligned to a reference DNA sequence result in the alignment being updated rather than recomputed from scratch.
Converted the view of alignments to a reference DNA sequence to a display parameter that is restored the next time a file is opened.
Enabled the import of features from BED, GFF3, and GTF formats.
(Requested by Alison Pidoux, Eddy Risseeuw, Maria Gonzalez, Jonathan Woodsmith, Erin Boyle Anderson, Yun Wu, Patricia Baker, Amyris, Yaara Yoren, David Kovalic, and Joe Georgeson)
Added a dedicated dialog for import of protein sequences from UniProt.
Enabled SnapGene to track the dates when primers are added to a sequence, and to sort primers by Date Added in Primers view.
(Suggested by Tim Rand and Steven Erickson)
Enabled SnapGene to open Vector NTI .cep contig assemblies directly.
(Requested by Wouter Pos)
Enabled SnapGene to open SAM / BAM contig assemblies directly.
Enabled SnapGene to import from and export to SAM/BAM alignment formats.
(Requested by Zhonggang Hou)
Enabled SnapGene to open GCG (Genetics Computer Group) encoded DNA and protein sequences and archives directly.
Allowed sequences in SAM / BAM files to be imported for alignment to a reference DNA sequence.
Enabled GCG and PIR / NBRF content to be pasted into the New DNA / Protein file dialogs.
Added an importer for Genome Compiler project and cloning project files.
(Requested by Doug Daniels and Martin Schneider)
Enabled the import of open sequence files for aligning to a reference DNA sequence.
Added buttons for moving selected sequences to the top or bottom of the list when first specifying sequences for a multiple sequence alignment.
Added the ability to copy DNA selections as RNA by holding the Opt/Alt key.
(Requested by Karl Brune)
Added New England Biolab's "λ DNA – Mono Cut Mix" ladder.
(Requested by Shari Carmon)
Enhancements
Added the ability to use Shift + Enter to navigate to previous search results.
(Suggested by Karl Brune)
Increased flexibility when exporting multiple sequences from a collection.
(Requested by Iris Dotan and Frank Thieme)
Ensured that when saving a collection, if the chosen collection name already exists, an option is provided to choose an alternative name instead of simply appending a number at the end.
(Requested by Carles Alvarez)
Added the ability to adjust the default start codons for newly entered and imported DNA sequences.
(Requested by Tim Barnett)
Dramatically sped up opening of large FASTA archives.
(Reported by Sierra Dargan)
Enabled the labeling of all or no lanes containing MW markers as "MW" when simulating an agarose gel.
(Requested by Brianna Bibel)
Added "Go To..." to the Find bar menu.
(Requested by Charles Zhu)
Made numerous significant optimizations
(e.g., when opening, importing, or interacting with sequences).
Made various textual, color, icon, and visual alignment enhancements.
Improved progress indicators when computing multiple sequence alignments.
Provided the option of computing a faster MUSCLE alignment if the full computation would take a long time.
Improved residue tooltips in multiple sequence alignments.
Enabled the default sorting option to be specified for a collection.
Added tooltips to various controls to indicate the associated keyboard shortcuts.
Added the ability to insert symbols into the name of an aligned sequence.
Preserved custom map labels when importing sequences for alignment.
Provided the option to replace the embedded display options with preferred display options when importing from Addgene or SnapGene.
Configured the import of multi-sequence archives to generate SnapGene collections, thereby allowing for quick browsing and searching of the converted archives.
(Requested by Tijs van den Bosch)
Improved security by using https for all network communication.
Ensured that localized dates are shown using the preferred format.
Added convenient controls for extending the selection in the Select Range dialog.
Improved the workflow when batch converting files.
Ensured that when the top toolbar is hidden, formatting controls are still available in the Description Panel.
Switched to the https secure network protocol for all forms of network communication.
Added a keyboard shortcut for "Show Alignments".
Fixes
Improved the import of GenPept files when computing a multiple sequence alignment.
(Reported by Junwei Ji)
Prevented a hang and eventual crash that could occur if several features are in frame with each other in a circular sequence.
(Reported by Pedro Olivares)
Improved the Cut button icon clarity using the small size on Retina displays.
(Reported by Pedro Matos)
Improved MW accuracy for ORFs and translated features containing ambiguous amino acids, as well as Properties view in protein windows and Primers view in DNA windows.
(Reported by Andriy Volkov)
Fixed various issues with the buttons for flipping inserts in the Gibson Assembly and In-Fusion Cloning dialogs.
(Reported by Andreas Kjaer)
Improved stability when editing a collection's code number format.
(Reported by Viktoria Lytvyn)
Improved the decoding of XML-formatted content (e.g., DS Gene files) on Windows.
(Reported by Mary Russell)
Ensured visibility of small feature segments in a map.
(Reported by Cas Simons)
Fixed a regression to allow pasting of a fragment into an Insert tab of Actions > Restriction and Insertion Cloning > Insert Fragment(s).
(Reported by Rishikesh Ghogare)
Enhanced the stability of the multiple sequence alignment consensus display.
(Reported by Luca Jovine)
Fixed an issue with the "Save As" keyboard shortcut on Windows.
(Reported by Adi Millman)
Improved stability when aligning very low quality sequences.
(Reported by Chris Craddock)
Ensured that AanI will be displayed in the list box in the Simulate Agarose Gel dialog.
(Reported by Wulf-Dirk Leuschner)
Improved feature segment borders in Sequence view.
(Suggested by Carles Recasens Alvarez)
Improved the opening of Geneious files to support annotated sequencing data.
(Requested by Hai Ying Yuan)
Ensured that the application does not get stuck when renaming a primer in an Action dialog.
(Reported by Jordan Voisine)
Prevented the "Move" controls for aligned sequences from being disabled while viewing an alignment to a reference DNA sequence.
(Reported by Masa Esaki)
Fixed an issue with importing some accession numbers from NCBI.
(Reported by Ruanbao Zhou)
Prevented the mouse indicator from being erroneously shown outside the trimmed portion of an aligned sequence.
Improved the behavior of the top toolbar when working with multiple sequence alignments.
Added "Preferences" to the launch dialog Help button menu on Linux.
Allowed for a BOM at the beginning of a primer list when importing from a file.
Prevented MUSCLE from outputting partial results.
Prevented menu commands from being erroneously enabled after canceling out an export dialog.
Disabled the "Set as Default Parameters" button when it will have no effect in the Align Multiple DNA/Protein Sequences dialogs.
Enabled top toolbar menu commands listed under View → Toolbars while viewing multiple sequence alignments.
Corrected the ruler numbering when using the Edit DNA Ends and Add/Edit Primer dialogs.
Made it easier to double-click to select a word in a name field.
Configured the New Protein File dialog to accept pasted '?' characters and convert them to X's.
Fixed an issue with showing an enzyme set saved to a local file in a cloning dialog.
Enabled a trimming handle in an alignment to a reference DNA sequence to be clicked and dragged directly, without first assigning focus to that interface element.
Improved the Tab responses in multiple sequence alignment dialogs.
Prevented the logging out of macOS from being thwarted by open SnapGene files.
Disabled various commands such as Actions → PCR when a modal dialog is shown.
Removed code numbers warnings shown in the collection window list after the issues have been resolved using the Description Panel.
Fixed invisible checkmarks for items in menus on Windows and Linux.
Ensured that the Order button is hidden when toggling the top toolbar with rich text controls visible.
Fixed the Tools menu in the Launch window to hide nonessential items on Windows and Linux.
(Reported by Debra Hansen)
Improved the painting of bottom strand cleavage triangles when they overlap features in Sequence view.
Ensured that when features are hidden by default in the DNA tab of Preferences, they are still visible by default in the Browse Common Features dialog.
Prevented a crash that could occur when clicking widgets in the Edit Code Number Format dialog.
Enabled the display of unknown enzymes in History view.
Improved stability when quitting the application while a tooltip is visible.
Configured Sequence view to scroll automatically to a selected primer-primer fragment.
Ensured that Undo and Redo commands are cleared after a document is closed.
Enabled "Paste Reverse Complement" when a DNA search or primer sequence control has focus.
Enabled the proper action of "Export Selected File" when viewing miscellaneous files in a collection.
Corrected a regression to show an error message if the Make Protein command is invoked when there is no selection.
Made various stability enhancements.
Improved the selection bar display when multiple protein features of different types are selected.
Ensured that a file is not marked as unsaved after adding or removing enzymes from the chosen set.
Fixed an issue with showing history colors in History view when selecting consecutive operations.
Improved the highlighting of non-aligned primer bases in PCR product history colors.
Ensured that History view correctly displays the number of times an enzyme cut an ancestor sequence.
Improved rendering of the ruler for an aligned FASTQ read when aligning to a reference DNA sequence.
Ensured that various "Export" context menu actions do not result in the dialog instantly disappearing on macOS.
Removed the inappropriate watermark option from the Options dialog when exporting a gel image.
Prevented unexpected Undo/Redo behavior after adding files to a collection.

New in SnapGene 4.2.10 (Dec 21, 2018)

New in SnapGene 4.2.9 (Dec 8, 2018)

New in SnapGene 4.2.8 (Dec 6, 2018)

New in SnapGene 4.2.7 (Dec 4, 2018)

New in SnapGene 4.2.6 (Oct 3, 2018)

New in SnapGene 4.2.5 (Oct 3, 2018)

New in SnapGene 4.2.4 (Aug 20, 2018)

Enhancements:
Increased the maximum allowed primer length to 250 bases.
(Requested by Eduardo Rodenas Martinez)
Dramatically sped up opening of large FASTQ files.
(Requested by Alfonso Valencia)
Enhanced the "Make Protein" converter to transfer DNA colors to the protein sequence.
(Requested by Luca Jovine)
Allowed protein_bind features to be bidirectional.
Provided the option, when using Folders view in a collection, to rename a selected file or folder by tapping Enter/Return on macOS or F2 on Windows.
Enabled import from NCBI of the reverse complement of a range of bases by specifying the right endpoint first.
Enhanced the multiple alignment tool to accept sequence traces as input.
Ensured that the Find bar and search results remain visible when switching to another sequence file in a collection and then back.
Updated the common features database.
Updated MAFFT from 7.312 to 7.407.
Made various color, textual, and other visual enhancements.
Fixes:
Improved network communication on Windows.
(Reported by F. Javier Piedrafita and others)
Fixed an issue where changing the name of a new DNA or protein file after pasting in a GenBank or GenPept sequence resulted in all features being lost.
(Reported by C. Dustin Rubinstein)
Fixed numerous issues with using proper group and decimal separators for European users.
(Reported by Thomas Reinard)
Improved the import of primers copied to the clipboard from programs such as Excel.
(Requested by Leah Tait and others)
Fixed an issue that resulted in content in the Description Panel not being visible or displaying the wrong font.
(Reported by Peter Nguyen, Pratyush Routray, and Cole Peters)
Improved the editing of custom common features.
(Reported by Shahar Bracha)
Improved stability when running SnapGene on a case-sensitive APFS file system.
(Reported by Jason Eads and Unekwu Yakubu)
Improved the decoding of features in Geneious files.
(Reported by Christine Eyler)
Prevented duplicate annotations that could occur when detecting common features.
(Reported by Wulf-Dirk Leuschner)
Prevented false positives when searching a collection by sequence name.
(Reported by Melissa Stokes)
Enabled the pasting into various controls of text that begins with "<" and ends with ">".
(Reported by Wulf Dirk Leuschner)
Modified the feature translation context menu to include a command for adjusting feature translation options rather than generic translation options.
(Reported by Chris Tipper)
Restored the NEB "2-Log DNA Ladder", which is identical to the newly renamed "1 kb Plus DNA Ladder".
(Requested by multiple confused scientists)
Improved stability when running Clustal Omega on some Windows installations.
(Reported by Yaseen Mamoori)
Corrected a regression that resulted in the font size being too large when printing.
(Reported by Tausif Alam and others)
Corrected a regression with copying from SnapGene and pasting into programs such as Excel.
(Reported by Leah Tait and others)
Ensured that the default directory for opening/saving/exporting is shown by default.
Improved the opening of RTF-encoded files.
Improved the warning system for shared licenses when the application has been idle for an extended period of time.
Prevented the selection (or selection bar) from being cleared inappropriately when editing a multiple alignment.
Improved stability when deleting residues within a multiple alignment.
Ensured that the selection bar is empty when a single row of gaps is selected in a multiple alignment.
Ensured that clicking the symbols button consistently pops up a dialog on Windows.
Prohibited renaming a folder in a collection to include a forbidden directory separator.
Fixed an issue with computing alignments with Clustal Omega, MUSCLE, and T-Coffee on Windows while logged in with a username that contains Unicode characters.
Ensured that when a DNA sequence is modified so that the number of feature segments drops to one, the remaining segment name is cleared.
Fixed an issue where -'s were shown when line breaking text in some places in the Japanese translation.
Improved the computation of sequence-profile alignments with MAFFT.
Fixed various issues with renaming a folder in a collection and then maintaining focus or retaining the selection.
Improved the behavior when using Find in Features view.
Ensured that features are consistently the appropriate height in circular maps.
Ensured that an amino acid name is displayed in Sequence view when a codon spans two adjacent translated features.
Improved stability when opening certain files.
Corrected the "Go To" dialog to show a blinking cursor instead of "1" when first opened.
Improved the behavior when creating or choosing a new Main Collection on Windows.
Fixed an isolated pliancy issue on macOS with Features and Primers views.
Corrected the behavior when Cmd/Ctrl-clicking feature names in Features view.
Ensured robust alignments with T-Coffee when the user account has spaces in the username.

New in SnapGene 4.2.3 (Aug 20, 2018)

New in SnapGene 4.2.2 (Jul 23, 2018)

New in SnapGene 4.2.1 (Jul 13, 2018)

New in SnapGene 4.2.0 (Jul 9, 2018)

New in SnapGene 4.1.9 (Apr 23, 2018)

New in SnapGene 4.1.8 (Apr 10, 2018)

New in SnapGene 4.1.7 (Mar 6, 2018)

New in SnapGene 4.1.6 (Feb 22, 2018)

New in SnapGene 4.1.5 (Feb 5, 2018)

Enhancements:
Preserved history colors for the selected operation when printing History view.
(Requested by Edward Wallace)
Enhanced placeholder files to support custom map labels and aliases.
Added WATSON MW Markers.
(Requested by Rui Tada)
Added Genessee Scientific MW Markers.
(Requested by Aaron Miller)
Added G-Biosciences MW Markers.
Fixes:
Ensured that bottom strand features are always imported from NCBI.
(Reported by Christiane Widmann)
Removed inappropriate quotes when exporting /number qualifier values to GenBank format.
(Requested by Simon Zumkeller)
Updated restriction enzyme website URLs for New England Biolabs HF enzymes and Promega enzymes.
Enhanced opening of GenBank files to omit placeholder values (".") in references.
Ensured that "Direct Submission / Exported by SnapGene" references are ignored when importing from text formats.
Fixed an issue with opening some Geneious files.
Improved the retention and updating of code numbers when adding sequences to a collection.
Corrected the display of mismatches and aligned bases for certain reverse aligned sequences.
(Reported by Leonid)
Fixed a regression with modifying the Description or Collection Author in a collection.
Enhanced the collection List view to support Page Up, Page Down, Home, and End keys.
Ensured that the collection toolbar navigation Back/Forward buttons autoscroll in List and Folder views.
Improved stability when closing a collection.
Added a clean-up step in the collection interface when rendering the Description and Comments fields after switching between sequences.
Ensured that the font size setting is respected when printing History view.
(Reported by Edward Wallace)
Improved the consistency of displaying primer Tm and length for the primer controls in various manipulation dialogs.
Corrected an issue where changing the name of the Product in the Overlap Extension PCR dialog did not update the name as shown in Map view.
Prevented the occasional display of a "Sorry, could not create collection." message when a collection actually was created.
Improved the behavior of the importer for certain GCK files.
(Reported by Tiffany Su)

New in SnapGene 4.1.4 (Jan 11, 2018)

New in SnapGene 4.1.3 (Dec 23, 2017)

New in SnapGene 4.1.2 (Dec 6, 2017)

New in SnapGene 4.1.1 (Nov 30, 2017)

New in SnapGene 4.1.0 (Nov 8, 2017)

New Functionality:
Enhanced collections to support a folder view of the files.
Added support for formatting and updating code numbers for sequences stored in collections.
Provided the option of marking sequences in a collection as part of a "Working Set" that can be easily viewed and manipulated.
Added the ability to drag files from a collection in order to (a) copy them to another location or collection, (b) move them to the Trash, or (c) attach them to an email message.
Added an undoable "Trim History Tree" command to the pull-down menu at the top right of History view.
Added a "Batch Trim File Histories" command to the File menu.
(Requested by Dan Piraner)
Added a new preference for automatically trimming the history of a sequence.
(Suggested by Dan Piraner)
Added the ability to choose enzymes that are palindromic, uninterrupted
(no internal N's), or nondegenerate (A, C, G, and T only) to the Choose Enzymes dialog.
(Requested by Vadim Timerbaev)
Added the option to import only primers that have a unique binding site.
(Requested by an anonymous customer)
Added absorbance values to the Properties tab for protein sequence files.
(Requested by Genevieve Labbe)
Added an "Import from Another File" button to the "Edit References" dialog.
(Suggested by Karl Brune)
Added "Date Created" as a sortable field when viewing a collection.
(Requested by Seth Goldman)
Enabled drag and drop of entire folders into a collection, and added an "Import Folders into Collection" command.
Added a context menu to the Browse Common Features dialog's list to enable editing or removing a feature, adding or removing a feature from the Favorites list, or opening a feature in a new window.
Added a "Duplicate in New Window" button to the Browse Common Features dialog.
Added the ability to order constructs directly from Synbio Technologies.
Enhancements:
Added support for multiple copies of the following qualifiers: allele, cell_line, cell_type, citation, clone, clone_lib, cultivar, dev_stage, experiment, function, host, isolate, lab_host, map, note, operon, PCR_conditions, phenotype, pop_variant, product, standard_name, strain, sub_clone, sub_strain, tissue_lib, tissue_type.
(Requested by Novozymes)
Added an option in Preferences for hiding the dashed line tick marks in sequence traces.
(Requested by Raffaele Fiorenza)
Reduced the minimum primer length for simulating mutagenesis.
(Requested by Sriram Vijayraghavan)
Improved the import of multiple files of varying types into a collection.
(Requested by Dan Kraut)
Added history colors for "Splice to Remove Introns".
Enhanced History view to display annealed oligo names.
Enhanced the Addgene importer so that when only a partial sequence is available, the topology is shown as linear, unless the backbone size is available, in which case a circular sequence padded with N's is shown.
Added the option of either preserving or updating the Date Added attribute when a file in collection is replaced by importing a new copy.
Ensured that after a common feature is edited, the list scrolls to show the edited feature if its name was modified.
Added "Swiss-Prot" to the list of formats offered when using Batch Convert File Format.
Made flipping a sequence trace an undoable action.
Added the option of requiring an exact match when replacing a feature name, primer name, or sequence author for sequences in a collection.
Added "Find Protein Sequence" and "Find Enzyme / Feature / Primer" commands to the Edit menu, by creating a cascading "Find" menu that improves discoverability.
Removed the compact format button from the side toolbar in the Anneal Oligos dialog because it provided minimal utility.
Added a warning to help prevent accidental pasting of a copied DNA sequence into the protein search controls.
Enhanced the Edit Feature dialog so that when using "Create Feature Segment", the list scrolls if necessary to make the created segment visible.
Added support for "Make Protein" from within the Browse Common Features dialog.
Added an alert when using a file with over 25 levels of ancestors, to indicate that simulations may be slow unless the history is trimmed.
Added a draggable splitter to the DNA feature dialogs to allow more space to view qualifier or segment information.
Added support for "New File From Selection" to the Simulate Agarose Gel dialog.
Made various optimizations.
Enhanced the color, alignment, and look and feel of buttons and other interface elements.
Reduced Linux download size.
Fixes:
Enhanced the GenBank importer to make better use of the SOURCE field.
(Requested by Novozymes)
Enabled the import of malformed GenBank files that lack a LOCUS line.
(Reported by Yoshihisa Oda)
Enhanced the reliability of the DNASTAR SeqBuilder and EditSeq importers.
(Reported by Kensuke Kataoka and Alex Justen)
Improved the reliability of recognizing the default genetic code when opening DNASTAR SeqBuilder files.
(Reported by Kensuke Kataoka)
Fixed an issue that prevented import of some Geneious files.
(Reported by Karl)
Fixed an issue with decoding GenBank files saved by ApE where N's were encoded as *'s.
(Reported by Bianca Nijmeijer)
Fixed an issue where remote recent files were sometimes not listed after quitting and starting the program.
(Reported by Dr Fanny Passot)
Fixed an issue with importing some records from NCBI.
(Reported by Thomas Folliard)
Improved the reliability of Undo/Redo after saving.
(Reported by Leonid Valentovich)
Enabled the Copy command in the Save/Save As dialogs, while disabling other irrelevant menu commands.
(Reported by David Scalzo)
Enabled use of the Copy keyboard shortcut from within the DNA feature dialogs.
(Reported by Juan Antonio Raygoza Garay)
Fixed an issue with importing some sequences from Addgene.
(Reported by Alexandra Iouranova)
Ensured that Sassafras-based installations will not consume a second license if a second copy of SnapGene is launched on the same computer.
Improved feature selection behavior so that when two overlapping features are selected, the union of the two feature sequences is selected.
Fixed the following unreliable shortcuts in cascading menus on macOS: File → Import → NCBI Sequence (Cmd+Shift+O) Edit → Copy Bottom Strand → 5'to 3' (Cmd+Shift+C) Edit → Find → [Various] View → Toolbars → Toggle [Top | Side] Toolbar All Commercial (Cmd+Shift+Opt+A) Nonredundant Commercial (Cmd+Opt+A) Unique Cutters (Cmd+Opt+1) Unique & Dual Cutters (Cmd+Opt+2) 6+ Cuters (Cmd+Opt+6) Unique 6+ Cutters (Cmd+Opt+7) Actions → Restriction Cloning → Insert One (Cmd+Opt+I) Actions → OE PCR → Overlap Two (Cmd+Shift+D) Tools → Align → Various
Fixed a number of memory leaks.
Made various stability improvements.
Fixed an issue where the "Save Changes" button was not always enabled when one or more files was selected while viewing "Unsaved" files.
Fixed an issue where history view did not clear when multiple files in a collection were selected.
Improved the process of assigning files imported into a collection to the correct area of the collection.
Fixed an issue with sorting collection files by date.
Fixed the macOS shortcut (Cmd+Backspace) discarding unsaved changes in Collections.
Fixed the macOS shortcut (Cmd+Backspace) closing a document without updating.
Edit → Select All and Edit → Invert Selection can now be used to select files in collections.
Ensured that feature directionality is preserved when exporting to GenBank format and re-importing.
Enabled the import of large Geneious files.
Disabled menu commands that should not be available in manipulation dialogs.
Removed nonfunctional SCF / ZTR / FASTQ options from the Batch Convert File Format dialog.
Fixed an issue where Edit → Find Protein Sequence could sometimes show the "Find Feature" controls instead while viewing a protein sequence.
Prevented a blue line from appearing inappropriately when clicking on the upper ruler in Sequence view.
Enabled the launch dialog to be closed on macOS even when it is configured to appear when all windows have been closed.
Modified the window announcing a new SnapGene version so that it no longer requires an immediate decision about updating.
Ensured that "Show Selected Features" and "Hide Selected Features" are properly enabled when interacting with protein sequences.
Fixed an issue where when importing multiple files into a collection, files could sometimes be shown in the wrong category.

New in SnapGene 4.0.8 (Nov 4, 2017)

New in SnapGene 4.0.7 (Oct 22, 2017)

New in SnapGene 4.0.6 (Oct 10, 2017)

New in SnapGene 4.0.5 (Sep 15, 2017)

New in SnapGene 4.0.4 (Sep 4, 2017)

New in SnapGene 4.0.3 (Aug 17, 2017)

New Functionality:
Added Thermo Fisher O'GeneRuler MW markers.
(Requested by Alexandra Iouranova)
Added TransGen Biotech MW markers.
(Requested by Xiong Qin)
Enhancements:
Added "TransGen Biotech" to the Sequence Author list.
Added support for "citation" and "PCR_primers" qualifiers.
Added support for the "/note" qualifier for J_segment features.
Improved the naming of imported features.
Fixes:
Ensured that code numbers and aliases are always shown in a collection list.
(Reported by Alina Goldstein)
Removed an outdated message about AgeI losing activity 37°C.
(Reported by Georg)
Fixed an issue where the keyboard shortcut for "Choose Enzymes" stopped working on Windows.
(Reported by Chris Jacobs and Fabian Bietz)
Improved loading performance of Recent File lists for network mapped drives.
(Reported by Maarten Rotman)
Configured the importer to open files written by CLC Bio 6.9 and prior.
(Reported by Dan Moran)
Enhanced the GenBank importer to convert a nonstandard qualifier to a /note qualifier that preserves the original qualifier name as a prefix.
(Requested by Novozymes)
Allowed iDNA and misc_difference features to be forward and reverse directional.
(Requested by Novozymes)
Fixed an issue when exporting feature names to GenBank/GenPept/EMBL/SwissProt format.
(Reported by Novozymes)
Ensured reliable import and export of strings enclosed in quotes in GenBank qualifiers.
(Reported by Novozymes)
Improved the reliability of importing and exporting GenBank feature names as well as deprecated and nonstandard feature types.
(Reported by Novozymes)
Fixed an issue where the wrong number of annealed bases could be displayed in the selection bar for a primer that has multiple binding sites.
(Reported by Chu Chen)
Enhanced how nonstandard feature types are migrated to /label qualifiers.
(Suggested by Novozymes)
Fixed an issue that could result in an enzyme being listed multiple times for a given restriction site or in the Choose Enzymes dialog.
(Reported by Nicola Zilio)
Improved the accuracy of extending selections by Shift-clicking while viewing an alignment.
(Reported by Leonid Valentovich)
Ensured that /note qualifiers are retained when decoding feature names from imported files.
(Requested by Novozymes)
Prevented the "File" and "Edit" menus from being shown behind other controls when using the Add/Edit/Duplicate Feature dialogs with a protein sequence.
(Reported by Icon Genetics)
Ensured that the selected file in a collection window is listed as an open file in Action window source menus.
Improved the responses of the collection window Replace controls.
Updated the collection window behavior so that after importing files, the display switches automatically to the “All” setting.
Ensured that keyboard shortcuts for switching enzyme sets work consistently while viewing a collection.
Prevented outdated messages from being shown after installing a software update.
Ensured that a linear map remains visible in Map view after exporting the map image.
Fixed an issue with displaying a map alias when exporting to a raster format.
Improved the margins for printed output.
Adjusted the Recent File menu tooltip position on Windows and Linux.
Improved the positioning of context menus in the collection window list.
Enhanced the GenBank importer to include a backslash (“/“) before a nonstandard qualifier during conversion to a /note qualifier.
Ensured that imported nonstandard or forbidden qualifiers are visible in a /note qualifier within the Add/Edit Feature dialogs.
Prevented the appearance of lingering phantom menus on macOS.
Ensured that if multiple suitable GenBank qualifiers are available for naming an imported feature, the first such qualifier is used.
Improved the import of partial sequences from Addgene.
Prevented the appearance of inappropriate transient messages while changing the list selection in a collection window.
Fixed an issue that prevented Action commands from working when no file was selected in an open collection window.
Prevented descents of characters from being clipped in various search fields.
Fixed the plain file icons in Recent Files menus on Linux.

New in SnapGene 4.0.2 (Jul 28, 2017)

New in SnapGene 4.0.1 (Jul 25, 2017)

New in SnapGene 4.0 (Jul 24, 2017)

New Functionality:
Added support for browsable “collections” that can be used to organize and sort DNA and protein files as well as miscellaneous files.
(Requested by dozens of customers)
Provided the option of defining a Main Collection that is accessible with dedicated commands.
Enabled rapid searching of collections by multiple criteria.
Enabled batch replacement within collections of DNA and protein sequences, feature and primer names, and sequence authors.
Added import and export options for protein sequences in Swiss-Prot format.
(Requested by Novozymes)
Added "Annotate Lowercase Regions as Introns" command.
(Requested by Helena Pires)
Added "Convert Introns to Lowercase" command.
Added support for sequence-free placeholder files.
Added optional “aliases” for display of alternative sequence names in Map view and in collection lists.
Enabled SnapGene to show dynamic alerts and other targeted messages.
Enhancements:
Enhanced sequence trace windows to support Edit → Make Uppercase/Lowercase.
Configured the Add Feature dialog so that mandatory qualifiers that have not yet been specified are shown by default.
(Suggested by John Ticehurst & Brendan)
Improved the GenBank and EMBL file format exporters to include primer data.
(Requested by Novozymes)
Allowed the preferences file to disable checking for and installing updates by setting "updates/disable=true".
(Requested by Novozymes)
Added a Cmd+Shift+K keyboard shortcut for "Set DNA/Protein Color”.
(Requested by Chandler)
Made various optimizations and textual and color enhancements.
Added Aldevron to the list of standard authors.
Added "Peak Height: #" information to trace viewer tooltips, and removed quality information from tooltips for failed called bases (N's).
Added the ability to override the Flexera server address and port number encoded within a license file, to facilitate moving a Flexera server or using multiple Flexera servers on disparate networks.
Updated and improved the Addgene plasmid importer.
Enhanced the feature dialogs regarding qualifiers that support multiple values, to support clearing a single qualifier value by clicking the minus button.
Enabled rapid insertion of a feature with the Insert Feature dialog by double-clicking within the list.
Added File and Actions menus to the launch dialog on Windows, so that the researcher can create a synthetic construct or plan a cloning experiment without first opening a file.
Enhanced manipulation dialogs so that the viewer contents are blurred before a template is specified, making it easier to read a message shown on top.
Added the option during logging off or shutting down of saving documents, discarding changes, or canceling the logout/shutdown.
Improved file associations and icons on Linux.
Optimized the import of primers from a list.
Improved reading and writing GenBank files, and prioritized use of the /label qualifier for storing feature names.
Updated the common features database.
Enhanced importing references from EMBL to use RG entries if no RA entries are provided.
Added biotechrabbit MW markers.
(Requested by Nadine Waeber)
Added Penn State MW markers.
Fixes:
Prevented an error message from being shown twice when attempting to edit a primer by double-clicking it within a manipulation dialog.
(Reported by Walter Bonacci)
Fixed various issues with feature and primer tooltips, and with exporting feature and primer qualifiers to GenBank and EMBL formats.
(Reported by Xavier Danthinne)
Improved the rendering of arrowheads for reverse directional ORFs that wrap around the numerical origin in linear maps.
(Reported by Max Juchheim)
Ensured that "Linearize by PCR" is automatically checked in a manipulation dialog after replacing an enzyme-based selection with a standard selection.
(Reported by John Murray)
Enabled the opening of older Geneious files.
(Reported by Sandra Malmgren Hill)
Restored consistent opening of .exdna files created by EnzymeX.
(Reported by Yuichiro Tsuchiya)
Fixed an issue that prevented "Open" links on web pages from working with SnapGene Viewer (and in some cases SnapGene) on Windows if the application was not already running.
(Reported by Henry Chu)
Fixed an issue where on NTFS volumes all files were falsely assumed to be readable and writable.
Ensured comma separation of large size values when exporting features.
Included "About SnapGene" as an entry that can appear in the list of open windows on macOS.
Ensured that minimizing or restoring a sequence trace results in an associated Chromatogram Data dialog being hidden/restored.
Improved the name in the Windows menu for an Align Full Sequence window.
Corrected a cosmetic issue when using the Replace Bases dialog for a sequence trace when no replacement was specified.
Prevented an entire sequence or trace from being deleted.
Ensured that Edit → Paste Reverse Complement pastes the reverse complement instead of the copied text when interacting with a sequence trace.
Enabled updates to local enzyme sets to be reflected in open manipulation dialogs.
Enabled Edit → Undo/Redo and the associated keyboard shortcuts to work while using the Insert Codons dialog.
Corrected a warning message about deleting the underlying sequence to specify “protein” rather than “DNA” when working with a protein sequence file.
Corrected a command in the Edit menu to read “Delete Primers” rather than “Delete Bases” if a pair of complementary primers is selected.
Corrected a menu command to read “Amino Acids” rather than “Bases” when working with a protein sequence file.
Fixed an issue in which selecting one or more primers that do not result in a DNA selection, and then holding Opt while clicking Edit → Delete Primers, would inappropriately generate a request for a DNA selection.
Ensured that "Zoom All" does not attempt to zoom windows that lack support for maximizing.
Enabled the "Zoom" and "Enter Full Screen" commands for all windows that support full screen mode.
Prevented the Restriction Enzymes window from allocating its own menu bar on macOS.
Ensured that the file extension for open sequence trace files is listed in the Window and Dock menus.
Prevented the "Set DNA Color" command from being enabled in read-only contexts such as manipulation dialogs where such changes would be lost.
Fixed an issue where View → Toolbars → Show/Hide Toolbar could not be used to toggle the side toolbar in manipulation dialogs.
Enabled showing/hiding and customizing a top toolbar in the New Synthetic Construct dialog.
Prevented recent files from being cleared if SnapGene is run from the command line with an option that exits the app before the Recent Files list has loaded.
Improved the behavior with code signing dll's and exe's on Windows.
Improved the default folder name when exporting two or more common features.
Improved the error message shown when attempting to register a network license from an invalid IP address.
Corrected the font size for aligned sequence names at the lower left of Sequence view on Windows.
Hid the scaling slider when showing an aligned sequence of a type such as FASTQ that has quality data but no trace data.
Improved the rendering of protein feature lengths when printing Features view.
Fixed an issue with the default Start folder name when installing on Windows.
Ensured that menu tooltips are invisible when a parent cascading menu is hidden.
Adjusted the Sequence Author combobox in the Description Panel to not display a clicked action text such as "Edit Sequence Author List...".
Ensured that undoing changes to fields in the Description Panel can be achieved by invoking the Undo action once rather than twice.
Corrected the algorithm for choosing a directory during repeated export of common features.
Prevented the side toolbar from being compressed when a window is resized.
Improved the automatic design of primers for Gateway fragments that are being inserted in the reverse orientation.
Corrected the display in Sequence view of selected segments of reverse directional features with run-on translations.
Prevented certain amino acids from being duplicated in the amino acid pull-down menu for the /transl_except qualifier in the feature dialogs.
Improved import and export of the /transl_except qualifier from other formats such as GenBank.
Ensured that if a mandatory qualifier remains to be specified, a different qualifier can be edited within the feature dialogs.
Improved the display of pliancy when mousing over the sequence name in a linear map.
Fixed an issue with the file icon and path when right clicking the title bar for a sequence trace on macOS.
Prevented an empty ruler from appearing in Sequence view of a cloning dialog when no template is loaded.
Ensured that DNA colors for top and bottom strands are exchanged when inserting a fragment in the reverse orientation.
Fixed various issues with viewing long sequence traces.
Made various stability improvements.
Prevented full sequence /source features from being exported when using the EMBL format to save or export DNA sequences.
Ensured that *'s in protein files can be imported.
Fixed an issue with writing the last base # per line when exporting DNA files to the EMBL format.
Ensured that the Browse Common Features and Insert Feature dialogs list the correct feature subset when the dialog is opened repeatedly.

New in SnapGene 3.2.1 (Aug 22, 2016)

New in SnapGene 3.2.0 (Aug 9, 2016)

New in SnapGene 3.1.0 (Mar 10, 2016)

New in SnapGene 3.0.3 (Jan 12, 2016)

New in SnapGene 3.0.2 (Jan 4, 2016)

New in SnapGene 3.0.1 (Jan 4, 2016)

New in SnapGene 3.0 (Jan 4, 2016)

New in SnapGene 2.8.3 (Nov 10, 2015)

New Functionality:
Beta version of the Japanese interface. In the Launch dialog, click Help → Language → Japanese.
Enhancements:
When editing references, clicking the "PubMed ID" field now auto selects the contents to make changing the value easier.
The "new version available" dialog was streamlined.
If your support contract has expired, we only inform you about major releases, not bug fix releases.
The Gateway donor vector pDONR222 was added.
Added 80 new features to the common features database.
Fixes:
Fixed an issue that prevented opening some older .dna files.
Fixed an issue that sometimes prevented performing Gibson Assembly and In-Fusion cloning when the template(s) had sticky overhangs.
Fixed an issue that could prevent Gibson Assembly or In-Fusion cloning when manually specifying the direction of inserts.
Improved the display of flipped and unflipped orientations of fragments in the Gibson Assembly or In-Fusion Cloning product tab.
Fixed an issue with printing the page header for Features and Primers views when also printing History view.
Improved the behavior of action dialogs that employ PCR when part of the DNA is selected.
Enhanced the alignment algorithm to avoid displaying a suboptimal alignment.
Fixed a stability issue when pressing or releasing keys.
Fixed a stability issue when exiting the Add/Edit/Duplicate Feature dialogs.
Ensured proper detection of software updates that are available only by renewing your service contract.
Ensured recognition of bottom strand underhangs when using the "To Uppercase/Lowercase" commands.
Ensured proper identification of the OS name for Windows 10 and OS X El Capitan when sending anonymous statistics.
Fixed a glitch where temporary files could contain multiple copies of sequence data and search indexes.
Fixed a rare issue where the Gibson Assembly and In-Fusion dialogs would generate and attempt to display a product when the ends did not actually overlap.
Prevented a potential issue with remembering the last used directory.
Enabled PCR in various circumstances when using a primer that can hybridize to either strand.
Improved protein searches to return matches that lie partially or entirely within a run-on translation.
Enabled the BLAST commands to be invoked while using the Description Panel.
Ensured that the selection in the Sequence view minimap always matches the sequence selection after interacting with an aligned sequence.
Fixed an issue where an aligned sequence and associated feature translations might not be displayed properly after modifying the reference sequence.
Improved the vertical appearance of the "Preview/Next Aligned Region" buttons when viewing an expanded aligned sequence.
Improved feature display when scrolling between regions of expanded alignments.
Fixed an issue where certain features did not display properly in circular maps.
Ensured that PubMed ID's would not be truncated when pasting into the Edit References dialog if leading spaces had been copied to the clipboard.

New in SnapGene 2.8.2 (Aug 18, 2015)

New in SnapGene 2.8.1 (Jul 17, 2015)

New in SnapGene 2.8 (Jul 2, 2015)

New Functionality:
Added an interactive minimap overview to Sequence view.
Enabled Map view to display either external plus internal feature labels, or only internal feature labels, or no feature labels.
Added a "Splice to Remove Introns" command.
Enabled cloning and PCR dialogs to remain open after generating the product, so that related procedures can be simulated quickly and easily.
Modified the Insert Fragment(s) dialogs to enable digestion of a linear vector.
Enabled individual features to be prioritized for display in maps.
Added a "Delete Trimmed Bases" command for cleaning up the display of alignments.
Modified the display of aligned sequences in Map view to show insertions as inverted triangles.
Enabled maps and history to be exported as grayscale images.
Added a "Hide Aligned Sequence" context menu command for Map and Sequence views.
Added Lowest, Lower, Higher, and Highest stringency trimming options for aligned sequence traces.
Added an "Open Recent" cascading menu to the top toolbar and the Dock menu on OS X.
Added an "Import from GenBank" command to the Dock menu on OS X.
Added a "Copy Map Label" context menu action.
Added a three finger tap gesture to look up enzyme information without modifying the selection.
Enabled bzip2 (bz2) compressed content to be opened directly.
Enhancements:
Improved history colors when flipping the sequence, adjusting the numerical origin, renumbering the bases, or changing the methylation.
Moved the aligned sequence tooltips in Map view to above the aligned sequences.
Improved the display of alignment gaps in Map view.
Sped up starting the application and showing manipulation dialogs.
Dramatically sped up the decoding of large archive files.
Sped up topology detection.
Sped up the opening of gzip (gz) compressed content.
Improved the opening of large FASTA archives and gz files.
Added file icons for the "Please choose", "Recent Files", and Windows menus.
Listed keyboard shortcuts in the Find menu.
Enhanced primer names and stems to turn red when mousing over an alternative binding site.
Modified Map view to show the sequence as two strands when custom DNA colors are visible.
Added "GenScript" to the Sequence Author list.
Added O'RangeRuler ladders from Thermo Scientific.
Added UBPBio ladders.
Updated the restriction enzymes and common features databases.
Various textual, color, and alignment enhancements.
Fixes:
Fixed a rare issue where the application could hang if an aligned sequence had no trace data and began with a non-matching N.
Improved the import of very large archives.
Enabled copy/paste of a primer-primer selection as a Find query.
Improved the behavior of the "Replace Original with Aligned" command.
Fixed various issues with displaying restriction sites when viewing a primer binding site in a circular sequence near the numerical origin in the Add/Edit/Duplicate Primer dialogs.
Fixed a stability issue if the current license expires while the software is in use.
Accelerated the display of feature pliancy and selection in Lines mode of Enzymes view.
Improved the import of text files with non-UTF file encodings (e.g., MacRoman).
Configured an Undo of a sequence edit to clear prior "Find" results.
Modified the behavior of the Back/Forward buttons in the Restriction Enzymes dialog to be simpler and more logical.
Prevented auto-complete from inappropriately listing headings and actions in the Sequence Author control in the Description Panel.
Fixed a stability issue when opening a .dna file not created with SnapGene.
Fixed a stability issue when moving, copying, and deleting files.
Prevented prior history colors from remaining visible after Undo of a sequence edit.
Ensured that an unsaved set of chosen enzymes will always be restored when opening a document.
Fixed a rare stability issue with showing the Genetic Codes dialog.
Fixed a stability issue with computing translations for features with introns.
Removed duplicate entries in the "Choose from" menu in the "Choose Enzymes" dialog.
Fixed a rare issue where a download progress dialog could be shown while the New Version Available window is visible.
Fixed a stability issue when using a context menu to remove an aligned sequence.
Made the Make/Edit/Duplicate Primer dialogs more compressible so that they fit completely on small screens.
Fixed a rare stability issue.
Improved “primer” feature import from VNTI .ma4 archives to show the imported items as primers.
Ensured focus transfer to the next window down when the top window is closed.

New in SnapGene 2.7.3 (May 29, 2015)

New in SnapGene 2.7.2 (Apr 28, 2015)

Enhancements:
You can now use Cmd+D on Mac to activate "Don't Save" when attempting to close a file with unsaved changes.
Added MW Markers from Axygen
Added MW Markers from Biozym
Improved detection of lacZ-alpha.
Improved default placement of windows.
Bug Fixes:
Fixed a crash that could occur while using the Simulate Agarose Gel dialog and switching between showing simplified and full primer duplex structures.
Fixed a regression where the option of regenerating the enzymes used to digest the vector was not offered when designing primers for InFusion cloning.
Fixed a bug where unsaved annotations were not reflected in history or transferred to the product when using a fragment directly when simulating Gibson Assembly or InFusion cloning.
Fixed a bug with showing some primer binding sites.
Fixed a bug where designed primers sometimes did not use the desired and required Tm.
Fixed a bug that prevented simulating Gibson Assembly using fragments(s) with 3' A or G overhangs.
Fixed a bug that resulted in an incorrectly generated Entry Clone when linearizing the attB insert within the BP and BP + LR cloning dialogs.
Fixed a bug that sometimes prevented simulating BP cloning when digesting the BP insert with an enzyme that cuts multiple times.
Removed a partially shown color button in the side toolbar of the Primer and Edit DNA Ends dialogs.
Fixed a bug that prevented attempting to destroy a restriction site at the numerical origin by selecting it and pressing the Delete key.
Updated KflI to indicate it is not Dcm methylation sensitive.
Fixed a crash that could occur after returning to interact with History view after resurrecting an ancestral sequence.
Fixed the crasher reporter Mac OS X Yosemite.
Fixed a potential crash in Features and Primers views when modifying annotations.
Hide the color mode and visibility controls in the Map & Sequence Options dialog when using an embedded sequence, e.g. while using a cloning dialog.
Fixed a bug where using a mouse wheel to scroll up or down after showing the zoom controls but not zooming could result exiting out of zoomed mode.
Fixed a bug where it was not possible to click on feature names outside a circular map or above a linear map if shown enzymes and primers were both turned off.
Fixed a bug where if using Gibson assembly to assemble a linear product, if the first amplified fragment wrapped around the numerical origin the product was incorrectly shifted and circular.
Fixed a bug where if using Gibson Assembly to assemble a linear product, sticky overhangs and endpoint modifications in the first and last fragment were not properly migrate to the product.
Fixed a bug that prevented using Gibson Assembly to assemble a linear product if either end of the product was covalently closed.

New in SnapGene 2.7.1 (Mar 9, 2015)

New in SnapGene 2.7.0 (Mar 6, 2015)

New Functionality:
Substantially improved look and feel on retina displays.
DNA colors
Primers colors
Edit multiple primers
Added Copied Primers (Cmd+Opt+R)
Simulate assembling fragments via Gibson Assembly
Added warnings for out of frame translated features when overlapping, assembling, or ligating one or more fragments.
You can now paste GenBank, EMBL, or FASTA encoded content into the New DNA File and Insert|Replace Bases dialogs. Annotations will be preserved as if you had opened a gb/embl/fa file directly. Similarly you can now align with a copied FASTA, GenBank or EMBL sequence. The default name for a pasted New DNA File or aligned copied sequence has also been improved.
Open DNADynamo files
Open gzip compressed content (e.g. .fa.gz)
When simulating an agarose gel, you can now copy the gel image or fragment list.
Expanded the range of agarose concentrations supported when simulating gels.
Added numerous MW Ladders. (NZYTech ladders, PHENIX Research ladders)
You can now make feature(s) from selected aligned sequence(s)" via a new "Make Feature[s] from Selected Sequence[s]" command in the "Aligned Sequences" menu.
Added "Enter|Exit Full Screen" commands to the Window menu on OS X.
Added a "Show Chromatogram Data" context menu command for aligned sequence traces.
Added "Copy Feature Name" and "Copy Primer Name" context menu actions.
Added commands to the jump list shown when right clicking the application in the taskbar on Windows 7 and later.
Enhancements:
Improved detection of lacZα
When mousing over an enzyme that cuts more than once, the stem connected other restriction sites now also turn red.
Reduced the size of text and features in History view maps to facilitate showing more annotations in the shrunken maps.
Added an option on Windows to automatically minimize the Launch window when all windows have been closed.
Added the "NEB Stable" transformation strain.
You can now select gaps within features by Opt/Alt+clicking them.
Prevent TOPO TA cloning with primers that are phosphorylated.
Updated the TA "TOPO" and Gateway Donor vectors.
The ruler shown for translated features in Sequence view now shows a break if there is a discontinuity in the translation numbering.
Removed the "Enzymes" tab from the TA and GC cloning dialogs since restriction enzymes are never used.
Added a "PCR and Mutagenesis Tutorial Video" command to the "Actions" menu.
Improved the visibility of warnings shown within the status box at the lower right of manipulation dialogs.
Improved display of ladder fragment lengths in simulated agarose gels.
Added Cmd+Shift+[, Cmd+Shift+], and Cmd+Shift+# to switch lanes in the Agarose gel dialog. You can now use the swipe gesture as well.
When changing the % agarose concentration the fragments now animate to their new position.
Improved look and feel on OS X Yosemite. Unfortunately we can no longer support OS X Leopard and Snow Leopard.
SnapGene is now a 64 bit application on Mac OS X.
Extensive icon, textual, color, and rendering enhancements.
Added support for queueing when using a shared license.
Bug Fixes:
Fixed a bug where when importing primers from a list, if the primers list began with a "Name Sequence" line an error message would be shown before proceeding with showing the Add Primers dialog.
Fixed a bug that prevented shifting clicking letter codes from two different translated in-frame features.
Fixed a bug that prevented importing primers containing U's or I's from a list.
Fixed bugs with opening and pasting DNA sequences containing colons and other punctuation.
Fixed bugs with displaying origin-spanning and other complex multiple sequence alignments.
Fixed a crash when opening files with a one or more blank lines at the top.
Improved importing primers from a Vector NTI database and GenBank files exported from Vector NTI.
Fixed a bug where printing an agarose gel the length of amplified fragments was not listed.
Fixed a bug with simulating Gibson Assembly with one or more fragments with 5' overhangs.
Fixed a bug with simulating InFusion Cloning with one or more fragments with 3' overhangs.
Fixed a bug where when toggling the "5' Phosphorylated" checkbox in the Make/Edit/Duplicate Primer dialogs, the melting temperature was not recomputed.
SnapGene now refuses to open bz2 compressed content.
Fixed a bug that could result in a hang when trying to find data within an empty file.
Fixed a bug with showing history colors after deleting an arbitrary range of bases.
Fixed a bug where various Edit menu actions (e.g. "Copy Top Strand") sometimes were not be enabled when a selection was present.
Fixed a crash that can occur if you rename, move, or delete a file while it was open and you were using a modal dialog (e.g. Edit Primers).
Fixed a bug that prevented pliancy from being shown for inserts in the TA and restriction cloning overviews.
Fixed a bug where a non-specified gateway vector was shown in black instead of gray in the cloning overview.
Fixed a bug where after changing the transformation strain the "Hide/Erase" button in History view did not become enabled.
Fixed a bug where tooltips shown in the New/Insert/Replace Dialog and a few other places would continue to be shown if the window containing the associated label was hidden or closed while the tooltip was visible.
Improved file association registration on Mac OS X.
Fixed a bug where when displaying a reverse aligned sequence as a double stranded sequence the DNA shown could be incorrect.
Fixed a bug that could result in a crash if you closed a document while using the Edit and Duplicate Primer dialogs.
Fixed a crash that could occur when closing an open document with unsaved changes that is currently in use in a manipulation dialog.
Turned off changing a combo box selection using the mouse wheel.
Fixed a bug that prevented restriction sites close to the numerical origin from being shown in History view.
Fixed a bug with showing partial filling in when using the "Choose dNTPs" dialog.
You can now use Cmd+Shift+[5-9] to switch to such tabs in cloning dialogs that have many tabs.
Fixed a bug that prevented drag selecting from a site in main view in Enzymes view to a site in the mini map or vice versa.
Fixed a bug where agarose gel fragment endpoints were not printed correctly when the template was set to count from something other than 1.
Fixed a crash that could occur when pressing the left arrow key when a button has focus.
Fixed a crash that result from use core search algorithms.
Fixed a bug in Map and History views where using the "Edit Map Label" and other context menu commands sometimes resulted in the map being copied tot he clipboard as well.

New in SnapGene 2.6.2 (Dec 19, 2014)

New in SnapGene 2.6.1 (Dec 11, 2014)

New in SnapGene 2.6.0 (Dec 3, 2014)

New Functionality:
TA, GC and UA cloning.
Support for U's in DNA sequences.
You can now edit the color, type, directionality, and translated state for multiple features at a time.
(Requested by Tian Chi and Wulf Dirk)
Non aligned ends are now shown when viewing alignments in Map view.
(Requested by Devin Strickland, Bryan Strouse, and Janel Lape)
All mutations are now visible when viewing alignments in Map view.
(Suggested by Wulf Dirk)
You can now linearize a circular sequence at the location of a placed cursor.
(Requested by Diane Chauliac)
You can now directly circularize a selected restriction fragment. When attempting to circularize a PCR product with single 3' base overhangs, SnapGene now offers to remove those overhangs in order to make circularization possible. Finally, history colors are now generated when circularizing.
(Requested by Dan Kraut)
You can now export Map and History views at various resolutions. Improved support exporting transparent images. When exporting as TIFF, SnapGene now uses LZW compression and transparent TIFF's are now also supported.
You can now export Map view, History view, and agarose gels to the EMF vector format on Windows.
When copying a map or history to the clipboard a vector form of the data is now stored on the clipboard so elements can be moved or edited when pasting into programs like Microsoft Office or Adobe Illustrator.
Open EMBL formatted sequences and export sequences using the EMBL format.
(Requested by Iñigo Lasa, Colin Adrain, and Kobi Benenson)
You can now export sequences to the DDBJ format.
Added "λ DNA – HindIII/φX174 DNA – HaeIII Digest" ladder
(Requested by Brian Ayre)
Enhancements:
SnapGene can now automatically annotate common features when opening FASTA sequences and archives.
(Suggested by Willem-Jan Waterreus)
The "Anneal Oligos" dialog now auto populates if two primers are selected in an open sequence when the window is shown.
You can now include features added by NCBI when importing from GenBank.
Added the full template name to the tooltip shown when mousing over the list in the Simulate Agarose Gel dialog if the name is truncated within the list.
When exporting History view to PDF, we now use Portrait instead of Landscape orientation since it usually fits better that way.
Improved the default size of the "Manage Enzyme Sets" dialog.
After linearizing at any position other than the origin, Map view now defaults to showing a broken circle.
Various font, color, and textual enhancements.
Bug Fixes:
Fixed a bug that could prevent printing with network printers on Windows.
(Reported by Cassandra Diegel)
Improved exporting to GenBank to better conform to the standard and resolve various warnings when converting to EMBL when uploading files to EMBL-EBI.
(Reported by Kobi Benenson)
Fixed a bug where trace data for short aligned sequences could be shown at too low a resolution.
(Reported by Miguel Cardoso de Brito)
Fixed a bug that could result in primers not being transferred to an amplified product when using PCR based dialogs.
(Reported by Mathias Friedrich)
Fixed a bug that prevented opening some MacVector files.
(Reported by Hilary)
Fixed a crash that could occur while simulating various manipulations.
(Reported by Angika Basant)
Fixed bugs with visualizing insertions at the numerical origin and replacing the original with the aligned sequence under such circumstances.
(Reported by Jason Niehaus)
Fixed a bug where if no attB inserts are to be amplified by PCR, when clicking "Choose attB Primers" SnapGene should pop up a message instead of doing nothing.
Fixed a bug with deselecting primers in Primers view by Cmd/Ctrl clicking.
Fixed a bug where primers were lost when using the "Replace Original with Aligned -> Make New File" command.
Fixed a bug with replacing and existing license file on Windows.
Fixed an erroneous error message that would show up (invalid license file) if installing the license file fails.
Improved exporting to SVG. (The bounds of the exported content are not set so scrolling, if necessary, is much improved).
Fixed a bug that resulted in "Copy Map" to sometimes be disabled while viewing Map view.
Fixed a bug where the default filename when using Save As was sometimes incorrectly set to "Untitled" on Mac OS X 10.9 and later.
Fixed a bug that prevented opening GenBank files when filtering files in the Open File dialog to "Sequence Files".
Fixed a bug where when simulating a manipulation using an open document with unsaved case changes, those changes were not reflected in a resurrected ancestor.
Fixed a bug where unsaved case changes were not properly reflected when exporting to FASTA or plain text.
Fixed a bug when annealing oligos I's were not converted to N's as expected.
Fixed a hang when deleting bases from a single strand from an end that is currently covalently closed while using the Edit DNA Ends dialog.
Fixed a bug where when enlarging the Edit DNA Ends dialog, additional space not used entirely for viewing the upstream and downstream ends.
Fixed a bug where if a mixture of colored and non-colored features were selected when triggering "Features -> Feature Color" no option should be checked by default.
Fixed a cosmetic glitches with rendering ovals and header buttons.
Fixed a bug where an error message was shown twice when trying to open a GenBank file that does not contain a nucleotide sequence.
Fixed a crash that could occur when importing a GenBank archive that contains on or more empty sequences (aka sequences without nucleotide data).
Fixed a crash that could occur while viewing raw sequence trace data.
Fixed a bug where if enzymes were off and you opened and then canceled out of the Choose Enzymes dialog SnapGene would offer to turn on showing enzymes.
Various stability fixes.
Fixed various memory leaks.

New in SnapGene 2.5.0 (Sep 10, 2014)

New Functionality:
Gateway Cloning
You can now insert or ligate up to eight restriction fragments.
You can now overlap up to eight fragments when performing Overlap Extension PCR.
InFusion Cloning now supports up to 8 fragments.
Print or export an inverted agarose gel.
Import a Range of Records from GenBank.
Import a region of a sequence from GenBank.
Import one or more primers copied to the clipboard.
Improved importing from Vector NTI Databases and ma4 archives to include sequence history, creation and modification dates, the sequence author, user comments, as well as maintain the creation / modification date and time in the resulting .dna files that are produced.
Added Thermo Scientific's "GeneRuler™ High Range DNA Ladder"
Added KAPA Biosystems' Express and Universal ladders.
Added Fisher Scientific Ladders.
Added SERVA DNA Ladders.
Added Thermo Scientific's MassRuler ladders.
Enhancements:
Reorganized the Choose Restriction Enzymes dialog to make it easier to find/use the controls for automatically select enzymes based on a criteria.
The number of binding sites are now shown in primer tooltips.
Increased the maximum number of recent documents listed to 25.
Enhanced the GenBank importer to decode base numbering if specified in a REGION indicator within the ACCESSION section.
SnapGene can now open malformed GenBank files produced by Vector NTI Express.
Added a yellow warning to the Add/Edit/Duplicate Primer dialogs when a primer has multiple binding sites.
Enhanced the look and feel of directionality buttons when a window loses focus.
Now decoding /Design_Description qualifiers in VNTI files as /note qualifiers.
Improved the mouse cursor while over or dragging a splitter.
Improved Actions menu layout.
Various optimizations, textual and tooltip enhancements.
Bug Fixes:
Fixed a bug where selected non-cutters were not listed when printing Agarose Gels.
Fixed a bug where feature names could overlap each other in circular maps.
Fixed various bugs with creating features from an enzyme selection whose right end is the numerical origin.
Fixed a bug where full-sequence "source" type features were changed to "misc_feature" when exported using the Vector NTI GenBank format.
Fixed a bug with copying while using the Edit and Duplicate Primer dialogs.
Fixed a bug that could result in bogus primers being shown for the current sequence in History View and a crash that could occur while interacting with these bogus elements.
Fixed a potential hang that could occur while importing VectorNTI databases.
Fixed a bug where after editing the list of MW markers, the pull down menu did not resize.
When closing a window, the next visible window is now automatically active.
Fixed a bug where when saved enzymes sets were modified, these changes were not shown in an already open PCR, Overlap Extension PCR, Mutagenesis, InFusion Cloning, or Gibson Assembly dialog.
Fixed a weird glitch where buttons in the launch dialog in addition to others would appear to disappear when the window lost focus.
Fixed a bug that prevented the Cmd+[ and Cmd+[ shortcuts from activating the Back/Forward buttons in the Restriction Enzymes dialog.
Fixed a bug where copying from the primer sequence controls copied invisible formatting to the clipboard.
SnapGene now refuses to open GenBank Protein sequences, informing the user that they are not yet supported at this time.
Fixed a regression with drawing rounded ovals used for example for mouse position indicators.
If a custom map label is used in Map View, we now use that custom map label for the root node in History View as well.
Fixed a crash that could occur when performing range limited a highly degenerate MICA search.
Fixed a bug that prevented alignment directionality symbols from showing up properly when printed to PDF on 10.9.
Fixed various glitches with printing the aligned sequences summary when printing Sequence View.
SnapGene now opens sequences full screen more smoothly on Mac OS X.
Fixed a bug that could result in aligned sequences reporting incorrect dates.
Fixed various bugs with pressing and releasing Opt/Alt and updating menu actions.
Fixed a regression that prevented "Go To" from working while viewing a sequence trace.
Fixed various bugs with printing zoomed alignments.
Fixed a bug that prevented "Replace Original with Aligned Sequences" from proceeding when using two more compatible aligned sequences if some but not all align around the numerical origin.
Fixed a bug that could cause a list selection to change when activating a window on Mac OS X.
Fixed a bug where when selecting an externally placed feature name in map view, the wrong DNA range was selected.
Fixed various bugs with viewing origin-spanning alignments as double stranded sequences.
Fixed a potential crash that could occur while trying to print on Mac OS X.
Fixed a crash that could occur while using Sequence View.
Fixed a crash that could occur while simulating agarose gels.

New in SnapGene 2.4.3 (Jul 3, 2014)

New in SnapGene 2.4.2 (Jun 13, 2014)

New in SnapGene 2.4.1 (Jun 10, 2014)

New in SnapGene 2.4.0 (Jun 2, 2014)

New Functionality
A 5’ overhang can be blunted by either filling in or chewing back.
A DNA sequence can be exported to a GenBank-style file that is optimized for import into Vector NTI.
Clone Manager individual primer files (.pd4) can be opened directly, and primer collection files (.px5) can be used for import into SnapGene.
You can now manually trim an aligned sequence by selecting the range to be trimmed off, then clicking "Aligned Sequences -> Trim Selected Range".
You can now linearly ligate up to four fragments.
You can now search for the amino acid "X" by using quotes.
The MW of amino acid selections are now show in the selection bar.
For a feature in the first row of a map, if there is not enough room to show the name within or along side the feature, the name is now displayed outside the map.
History View now displays how a sticky end was blunted.
History View now lists the names of primers used during PCR.
When features or primers are viewed in a DNA file, imported from a list, or when detecting common features, a new button at the top left provides options for quickly checking and unchecking the listed items.
If you hold Alt/Opt, you can now "Copy Transparent Map" or "Copy Transparent History". This works for the Edit menu, the top toolbar button menu, and right click context menus in Map and History views.
Enhancements:
Improved detection of Gateway recombination sequences.
Improved opening of GenBank files exported by Vector NTI including sequence name, author, creation and modification dates, and feature names.
Improved opening of GenBank files exported by Serial Cloner including feature visibility, names, colors, directionality, and descriptions.
Improved support for QHD displays on Windows.
When exporting the default directory is now the last directory content was exported to. In addition the last format used is now the default format.
The yellow messages that indicate a number of enzymes, features, or primers are not displayed on map view due to limited space now show a tooltip when moused over that indicates which enzymes, features, or primers could not be shown.
Added support for the "Candidate Division SR1 and Gracilibacteria" genetic code.
Sped up alignments of fairly large sequences (e.g. 40 Kbp) against very large reference sequences (e.g. chromosomes).
Added links to Translations and Alignments tutorial videos.
Various color and textual enhancements.
Bug Fixes:
Fixed glitches with opening GenBank files that contain tab characters.
Improved decoding feature names from GenBank files.
Fixed a bug where features might not be transferred to the product when simulating PCR using overlapping primers that mutagenize the sequence.
Fixed a bug where PCR based dialogs would sometimes complain that a primer pair was not suitable for PCR when despite overlapping binding sites PCR was possible because the template was circular.
Removed nonfunctioning File and Edit menus from Make/Edit/Duplicate Primer dialogs on Windows.
Fixed a bug where if a non-native file was chosen as the template or vector in any of the manipulation dialogs, features would not be transferred to the product while simulating cloning, PCR, etc.
Fixed a bug where long sequence and ancestral sequence names could be cut off when shown in History View.
Fixed detecting custom 7 and 8 bp custom common features.
Fixed issues with annotations are not shown, would you like to display them type messages on Windows.
Fixed a bug where horizontal scrolling switched tabs in the Preferences, Map & Sequence Options, Primer and Chromatogram Data dialogs.
Disabled the "Select All" button while using the "Add Features/Primers" and "Detect Common Features" dialogs since selections are not allowed.
Fixed a bug that made it impossible to use a non-native file as the vector in the InFusion Cloning and Gibson Assembly dialogs.
Fixed a bug that could result in a crash when editing feature translation options for 1 and 2 bp features.
No longer listing translation qualifiers (codon_start, transl_table, translation) in Features View for features that are not marked for translating in Sequence View.
Fixed various bugs with opening some rich text encoded files.
"Apply this genetic code to existing features" did not properly update feature translations, mark the sequence as modified, or support Undo/Redo.
Fixed a glitch where an empty COMMENT or DEFINITION was sometimes exported to GenBank formats.
The "Reset Warnings" button in the Preferences dialog is now disabled if no warnings have been turned off.
Fixed a bug that resulted in features now being shown for the current sequence in History View after transforming into another strain, changing the methylation, or other changes that don't result in actually changing the underlying DNA.
Disabled "Edit -> Select Range" while using the Detect Common Features and Import Features/Primers dialogs.
Fixed various glitches with shift-clicking fragments while using the Simulate Agarose Gel dialog.
Fixed the MW for amino acids "X" and "B"
Fixed a bug where history colors might now shown when using mutagentic primers to simulate PCR.

New in SnapGene 2.3.5 (May 9, 2014)

New in SnapGene 2.3.4 (May 9, 2014)

New in SnapGene 2.3.3 (Apr 16, 2014)

New in SnapGene 2.3.2 (Mar 27, 2014)

New in SnapGene 2.3.1 (Mar 27, 2014)

New in SnapGene 2.3.2 (Mar 21, 2014)

New in SnapGene 2.3.0 (Mar 13, 2014)

New in SnapGene 2.2.2 (Dec 16, 2013)

New in SnapGene 2.2.1 (Nov 30, 2013)

New in SnapGene 2.2.0 (Nov 30, 2013)

New in SnapGene 2.1.0 (Sep 17, 2013)

New in SnapGene 2.0.1 (Jul 30, 2013)

New in SnapGene 2.0.0 (Jul 25, 2013)

New Functionality:
Substantially improved alignment algorithm (better alignments, faster, supports sequences up to 1Mb)
Multiple sequence alignments with automatic trimming of aligned sequences
Added a "Clear All" button to the "Edit References" dialog.
You can now view chromatogram data by clicking the associated button while viewing a sequence trace.
Moved the "Add" button and added a "Remove" button to quickly adding/remove enzymes from Enzymes View.
Enhancements:
Improved predicted sequence trace quality
Substantially sped up scrolling while viewing alignments.
Enhanced the display of red boxes for discrepancies and yellow boxes for poor base calls when viewing alignments and aligned sequences.
If you select one or more codons and invoke "Make Feature", the feature will now be translated by default.
Improved sorting of features/primers by name.
Improved the organization of feature types in the pull down menu found in the Add/Edit feature dialogs.
Improved auto scrolling the list features in the "Browse Common Features" dialog to first feature with typed letter.
While a list view has focus, Edit->Select All is now enabled and will select the entire contents.
When adding a feature or primer or choosing enzymes, if the associate annotations are currently toggled off SnapGene will now offer to display them.
Moved BLAST, alignment, gel simulation, and other commands to a new "Tools" menu and improved the organization of the File, Actions and Help menus.
Improved the default filename when exporting features or primers.
Changed the GenBank format names to "GenBank (standard)" and "GenBank (enhanced)"
Updated the Restriction Enzymes database including: -website links for Fermentas enzymes -updated buffer information for NEB enzymes -added PluTI -removed BfrBI and Bsp143II (both long discontinued) -removed NEB as a supplier for BstF5I (long discontinued)
Added "Thermo Scientific (Pierce)" to the list of predefined authors.
Added "pUC19 – Sau3A I Digest" (General), "pHY Marker" (TaKaRa) and several Invitrogen MW Markers.
Added "Plant Cells" and "Schizosaccharomyces pombe" to list of organisms in the description panel.
Added "AviTag™" to the list of "Epitope and Affinity Tags" in the Insertions tab of the Primer dialogs.
Added the following E. coli Strains: EC100™, EC100™-T1R, EC100D™ pir+, EC100D™ pir-116, EPI300™, and EPI300™-T1R
Added "ATG + GTG" and "ATG + GTG + TTG" to the list of start codon options in the "Translation Options" dialog.
Added a "Registration..." link to "Help" menu in the launch dialog.
Speed up fetching DNA for large sequences.
Enhanced plasmid topology detection.
Various color, font, textual and alignment enhancements.
Bug Fixes:
Added line breaks when exporting to FASTA
Fixed a bug with decoding feature ranges from Vector NTI files
Fixed a bug where when opening a GenBank file if the sequence length reported in the LOCUS field up top was incorrect due to a bug in Vector NTI, SnapGene might not import the entire sequence.
Fixed a bug where SnapGene would fail to properly open files with .dna or .index extensions that are not SnapGene files.
Fixed a bug with displaying features.
Fixed a bug where after aligning with a sequence trace, SnapGene did not default to that directory when aligning to additional sequences or opening new files.
Fixed a bug where attempting to add primers that hybridize around the numerical origin could cause the application to hang if features were visible just right of the origin.
Fixed a bug that allowed multiples copies of SnapGene to be run simultaneously.
Fixed a bug where after closing the Noncutters dialog, hiding and then restoring a document window would result in the Noncutters dialog reappearing.
Fixed a bug with decoding features and other data from Clone Manager files.
Fixed various glitches when closing open documents that have changes while they are shown with a manipulation or other dialog.
SnapGene now detects and refuses to open GIF, JPG, PNG and TIFF and SeqBuilder Project files.
Right clicking on the reference sequence when aligning with a trace and invoking "Select Range..." had no effect.
Fixed a bug where "Find Protein Seuqence" was offered when pasting a sequence that contained non DNA characters into the Trace Viewer and Align dialog's find controls.
Fixed a crash when computing alignments
Fixed a memory leak associated with computing alignments.
Fixed a bug with computing alignments around the numerical origin.
Fixed a bug that could result in menu actions (e.g. Copy) being remaining disabled after a window is activated.
No longer embedding history summary if a sequence has no history or it has been erased.
The "Source Organism" menu now expands to a more reasonable size.
Removed white box at lower left of Enzymes View / Lines mode.
Improved inverting Feature/Primers selections, especially within Features and Primers views.
Fix a bug where when searching by DNA in Sequence View, if many features or enzyme sites are displayed the matching DNA might not be visible when scrolling to show a match.
Fixed a bug where when using the Add/Edit Primer dialogs, the Sequence View line width setting was inappropriately being used instead of fitting content to the space available.
Fixed alignment of fragment lengths in the Simulate Agarose Gel dialog when 10 or more fragments are generated.
Fixed a bug where feature cleavage arrows at sequence ends were not displayed.
Fixed a bug where the "Go" button was not disabled when no base was specified in the "Go To" dialog.
Fixed the bug where editable combo boxes display their content down too far.
Fixed a bug where case discrepancies would be shown in red as if they were actual mismatches.
Fixed a bug that prevented N-stretch insertions from being highlighted in red
Fixed various bugs that resulted in discrepancies from being displayed properly
Fixed a bug that prevented showing the genetic codes dialog when clicking alternative genetic code names within features view.
Fixed a bug where when transferring focus from the zoom controls back to a view the current document selection should not be cleared.
Fixed a bug where when the zoom controls have focus a document selection should be shown in gray not blue.
Fixed a bug where "Blast Selected DNA" was enabled when first opening a sequence trace despite the lack of a selection.
Fixed a bug where stop codons were included in the amino acid count in Feature tooltips.
Fixed a bug where MW should not be reported for feature segments with internal stop codons in Feature tooltips.
Fixed a crash that could occur while using using the Restriction Enzymes dialog.
Fixed a memory leak with freeing Trace objects where we predicted quality.
Fixed a bug with displaying quality of flipped sequence traces.
Fixed a crash that could occur when exiting out of a manipulation dialog.
Removed check for running copies during installation on Windows since this seemed to be creating more problems then it was worth.
Fixed a bug where after shifting the selection using the left/right arrow keys while viewing a sequence trace, subsequently using Shift+Left/Right to adjust the selection would cause the selection it to jump.
Disabled "Make Uppercase/Lowercase" commands when a selection is present in an aligned sequence or viewing a sequence trace.
Fixed a bug that in theory would allow you to create a sequence >= 1 Gbp by using the Insert/Replace file dialog.
When performing a paste or deletion on an aligned sequence we no longer trigger the cloning dialogs when enzyme sites are involved.
Fixed potential crash with Feature dialogs.
Optimized rendering the Sequence Viewer top ruler.
Added sanity check to avoid a crash while attempting to make a network connection.
Sped up viewing small sequences in Sequence view and displaying ORFs.
Fixed a bug with laying out feature names that could result in sequence view run into an infinite loop while horizontally scrolling.
Fixed various glitches that could result in laying out long lines in Sequence View.
Fixed a bug where when using infinite scrolling in Sequence View, toggling enzymes, features, primers, or ORFs would cause the view to scroll every so slightly.

New in SnapGene 1.5.3 (May 9, 2013)

New in SnapGene 1.5.2 (Mar 16, 2013)

New in SnapGene 1.5.1 (Mar 2, 2013)

New Functionality:
SnapGene now supports network and floating licenses for institutions.
Enhancements:
Improved the default filename when printing to PDF from the "Noncutters", "Genetic Codes", and "License Agreement" dialogs.
You can now trigger the "Select Range" action using the menu shortcut when focus is in the find controls, zoom controls, or "Description Panel".
Added message indicating references can be imported from PubMed.
Updated standard common features database.
Various textual and font enhancements.
Bug Fixes:
Fixed glitches with showing pliancy for the map label when it is placed below a circular map.
Fixed glitches with displaying enzymes and primers in broken circular maps.
Fixed a glitch that prevented selecting an entire linear sequence when first clicking the "End" label and then shift clicking the "Start" label.
Fixed a bug where when clicking "Set Default Sequence Author…" the associated field did not automatically get focus when the Preferences dialog was shown.
Fixed a bug where the most recent enzyme name used to cleave the downstream end of a linear sequence was not cleared when a double stranded selection at the downstream end was removed.
Fixed a bug where when using the Insert Fragment(s) dialog, if you flipped a fragment, then deselected the insert in the fragment list, when reselected the flipped state was not reset in the overview to reflect the state in the side controls.
Fixed a bug where the "Import from GenBank" command could sometimes fail to download a sequence.
Fixed a memory leak that could result in a crash when a file that was once open in a closed manipulation dialog is deleted or renamed.
Fixed a bug that prevented displaying a context menu when right clicking on DNA or empty space while using sequence view in a manipulation dialog.
Fixed a bug that prevented pasting into the feature segment endpoints within the Make/Edit Feature dialogs. (Reported by David)
Fixed a bug that could result in the omission of the sequence length in circular maps.
Removed ORF information from feature tooltips when the feature uses an alternative start codon and includes a full coding sequence.
Fixed a bug where after auto completing a "Laboratory Host Organism" or "Source Organism" in the "Description Panel", the auto completed value was not saved.
Fixed a bug where when changing the "Source Organism" to "Escherichia coli" a dialog would appear multiple times asking if you wanted to change the methylation if no methyl groups were present.
Fixed a bug where when viewing a broken circle map the correct top strand length was not shown.

New in SnapGene 1.5.0 (Feb 19, 2013)

New in SnapGene 1.4.1 (Jan 24, 2013)

New in SnapGene 1.4.0 (Dec 13, 2012)

New Functionality:
You can now scroll an entire sequence on one line in Sequence View.
SnapGene can now auto scale sequence trace data to correct for exponential decay.
SnapGene now supports just under 200 transformation strains.
You can now export specified feature data.
Primers can now be exported using a FASTA format
You can now copy feature and primer selections to the clipboard.
Added preferences for the look and feel of sequence traces.
Enhancements:
When zooming, sequence view no longer attempts to avoid scrolling the content displayed and instead updates as expected.
Added "Check for Updates..." to bottom of help menu in launch dialog Added URL's and buffer reactivity information for enzymes available from TaKaRa.
Updated the common features database
Opt/Alt+Delete can now be used to bypass warnings in all contexts, including deleting custom features while using Browse Common Features.
The Find controls while viewing sequence traces or aligning sequences are now hidden by default.
Substantially sped up opening and viewing files with large histories
When making a selection from within another view, or when using the Select Range command, Sequence View now attempts to scroll to display the entire range, not the last base (or in one case the 1st base).
When viewing large complex sequences, SnapGene should be more responsive while adjusting display options.
Optimized opening and interacting with sequences
By default only the first 5 rows of history are displayed by default for files with extensive history.
Enhanced the look and feel of the mismatching navigation buttons while using the "Align with Sequence Trace" command.
Enhanced positioning of the mouse position and drag indicators.
Expired and incompatible licenses are now automatically updated at startup.
Now sending license information when reporting crashes to facilitate contacting users and resolving problems that are encountered.
Streamlined the look of primer binding sites in map view.
Various textual enhancements
Bug Fixes:
Fixed various bugs when working with sequences over 9999 bases in length on Windows using Brazilian Portuguese
Fixed a bug that could result in crash when aligning sequences.
Fixed a bug that could result in a crash when opening GenBank, MacVector and ApE files.
Fixed issues with reading some FASTA, EditSeq, and GenBank files on and reading and writing custom enzymes sets on Windows.
Fixed a bug that could cause horizontal scrolling of sequence view to be sluggish, especially on computers with Retina displays.
Fixed a bug where if the first primer used for PCR binds to the bottom strand and the second primer binds to the top strand, the melting temperatures for the two primers were swapped in the primer controls in the PCR and other PCR based manipulation windows.
Fixed a bug where if two primers are selected the result in a full sequence selection, tapping the delete key should offer to delete the primers, not replace the selected bases.
Fixed a bug where "Primers" and other buttons in History View could shift or disappear after minimizing and restoring the window.
Fixed a bug where when a sheet was displayed, hiding and restoring the window could cause the sheet to turn blank or disconnect from the window.
Fixed a bug that could result in a crash when replicating feature regions when extending a sequence by linearizing with a sticky cutter or using partially overlapping primers to amplify a fragment.
Fixed a bug where when viewing incredibly large sequence (hundreds of millions of bases) with all enzymes displayed at the largest font size and a narrow window width it was impossible to scroll in sequence view.
Fixed various glitches with finding enzymes, features and primers.
Fixed a bug that could cause SnapGene to crash when toggling enzymes, features, primers, or changing display options in other ways while not viewing map view.
Fixed a bug where the Launch dialog would not reappear on Windows after canceling out of the "New DNA File" or "Import from GenBank" dialogs.
Fixed placement of "Show History" buttons below linear maps in history view.
Fixed a bug where if you transferred focus away from SnapGene using Alt/Cmd+Tab, then moved the mouse and transferred focus back to SnapGene, the ruler in sequence view did not properly show where the mouse until it moved again.
Fixed a bug that could result in a crash when selecting a non native file while using the Align with Trace, Mutagenesis, or Add Primer dialogs.
Fixed a bug where when using the "Select Range" and "Go To" commands the dialog incorrectly indicated the last base in the pull down menu and allowed entering values one greater then the actual sequence length or visible range.
Flipping a trace sequence is no longer an undoable action since it really is an unsaved viewing option. In so doing SnapGene no longer informs you the sequence is modified and asks to save changes before closing if all you have done is flip the trace sequence.
SnapGene now refuses to open files that contain no DNA segment or an empty DNA segment (e.g. that SSpa file sent to us by a user. SnapGene could crash later while open if it actually tried to navigate such a file).
Fixed a bug with opening or aligning to extremely degenerate DNA sequences.
Fixed a bug that allowed scrolling short sequence traces that should not require scrolling.
Fixed a bug where when using "Sort Feature List", a blank option was listed in each pull down menu.
Fixed a bug where when using "Sort Primer List", if you expanded the dialog to show all options a blank entry was listed at the bottom.
Fixed a bug that could result in a crash when closing a tabbed manipulation dialog.
Fixed a bug that could cause a crash when checking to see if a plasmid map name is under the mouse.
Fixed a bug that could cause SnapGene to crash when importing some files.
Fixed a bug that could result in a crash when quitting the application.
Fixed a bug that could result in a crash while using the Common Features dialog.
Fixed various bugs that could result in a crash when detecting an open file is moved or deleted.
Fixed a crash that could occur when using the keyboard to modify the selection while using Features or Primers views.
Fixed problems that could occur when exporting primers to a list if a primer name contains the chosen delimiter.
Fixed a bug where N's were copied as -'s for sequence trace selections.
Fixed a bug where a map label should not show pliancy until the window has focus.
Fixed a bug where in history view if the current sequence or an ancestor contained one or more periods in its name the part of the name could be omitted.
Fixed a crash that could occur when opening new files and checking for map name pliancy for a map was generated.
Fixed a bug where Save As from a trace window would not default to the proper directory.
Fixed a bug where when completely zoomed out some enzymes would incorrectly indicate that there are "No sites within the zoomed range".
Fixed a bug that could result in a crash when performing an alignment.
Fixed a bug with creating feature segments downstream of a feature gap.
Fixed a bug with updating feature translations when editing a feature with one or more introns.