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CodonCode Aligner Changelog

What's new in CodonCode Aligner 10.0.2

Feb 18, 2022
  • CodonCode Aligner version 10.0 introduces restriction cloning, sequence maps, support for separating alleles, and more.
  • More:
  • Show single letter amino acid translation on base level
  • Highlight start and stop codons in sequences
  • Show bases in customizable groups or without grouping

New in CodonCode Aligner 9.0.1 (Oct 6, 2019)

  • Better Base View:
  • CodonCode Aligner 9 introduces a new base view that displays features and restriction enzyme cut sites.
  • Clicking on a feature will select the features and the bases that it covers. Shift-clicking extends the selection. You can select a restriction fragment by first clicking on the restriction enzyme name, and then shift-clicking on a second enzyme name.
  • Mouse overs display information about the features and cut sites. A mini map at the top gives an overview of the features and allows quick navigation within the sequence.
  • The toolbar buttons on the left of the base view contain options to show or hide, or select specific features and enzymes, for example showing only enzymes that cut once.
  • Sequence Selection:
  • Aligner 9.0 adds the functionality to select samples and contigs based on length, name, sequence, direction and assembly status.
  • This new feature is especially useful when working with large projects and eleminates scrolling to select sequences.
  • You can use multiple of these selection methods at once by using the option to search in the current selection.
  • EMBL and Genbank Feature Support:
  • Newly added to Aligner 9.0 is the ability to export sequences in Genbank and EMBL format.
  • Also, all Genbank and EMBL features are imported in this Aligner version and can be displayed based on user preferences. Features colors are settable and features can be used to navigate and select bases.
  • More:
  • Select "Range of Bases": Select bases by entering the base numbers to select.
  • Improved clustering speed and accuracy
  • Change feature (tag) colors
  • Edit sample comments in the project view
  • New feature (tag) preferences that allow showing only specifc feature (types) in the project
  • Improved handling of ambiguities when searching for sequences

New in CodonCode Aligner 8.0.1 (Mar 8, 2018)

  • Dot Plots
  • The new functionality to create dot plots in CodonCode Aligner 8.0 allows you to quickly compare sequences for similarity and check for overlap.
  • Special about dot plots in Aligner is that you can compare several sequences at once. If multiple sequences are used to create the dot plot, you can choose the vertical and horizontal sequences.
  • Clicking in a dot plot will bring up the two sequences at that position in the alignment panel at the bottom of the dot plot. The blue background for matching bases makes it possible to quickly see which bases would align.
  • The dot plot is zoomable and can be printed. It also allows you to include the reverse sequence and to change the comparison word size.
  • Clustering Sequences:
  • Newly added to Aligner 8.0 is the ability to cluster nearly identical sequences, an analysis step frequently used in metagenomics. Aligner's default clustering algorithm can create larger clusters than other programs by carefully selecting optimal "cluster center sequences".
  • Identifying Sequences:
  • The new "Identify Sequences" function in CodonCode Aligner is intended for metagenomics projects, for example to identify species in an environmental sample by comparing 18S RNA sequences against databases like the SILVA database. Identification results can be hierarchically summarized by taxonomy.
  • Amino Acid Based Alignments:
  • Aligner 8.0 adds the functionality to create alignments based on amino acid translations using the program MACSE. MACSE accounts for the occurrence of premature stop-codons and frameshifts during the alignment. Alignments of coding regions with MACSE often have better placements of gaps compared to alignments created by Clustal or Muscle.

New in CodonCode Aligner 7.1.2 (Aug 28, 2017)

  • RFLP Analysis:
  • CodonCode Aligner 7.0 allows you to analyze your sequences for restriction fragment length polymorphisms. With this new feature you can compare cut sites for all samples in a contig and identify enzymes to use for your RFLP analysis. Generate a virtual gel of the expected results and print it to easily identify the lanes of your actual gel.
  • Aligner can automatically pick the enzyme that generates the most different cut result for your sequences. You can chane enzymes and display options for already generated results, or start a new analysis for the same contig to compare different results side by side.
  • Improved NGS Assembly"
  • CodonCode Aligner 7.0 adds a new "built-in" assembly algorithm for NGS sequence data. Compared to NGS assembly with SparseAssembler (introduced in CodonCode Aligner version 6.0, and still supported), the new built-in NGS algorithm can give significantly larger contigs and N50 numbers. The following table illustrates this, using bacterial genome data from the GAGE and GAGE-B test sets.
  • Actual difference will vary depending on the data set. For longer reads like the 250 base Illumina data in the Vibrio dataset, contig sizes and N50 numbers can be more than 10-fold higher for the new built-in algorithm than with SparseAssembler.

New in CodonCode Aligner 7.0.1 (Apr 21, 2017)

  • Introduces functionality for RFLP analysis and improved NGS assembly.

New in CodonCode Aligner 6.0.2 (Oct 22, 2015)

  • Fixes bugs introduced in version 6.0.1.

New in CodonCode Aligner 6.0.1 (Oct 22, 2015)

  • Primer Design:
  • Primer design in CodonCode Aligner 6 utilizes Primer3 to pick sequencing or PCR primers. Primer can be imported in the current project and are highlighted in the template sequence.
  • Create primer pairs for PCR at the optimal location within a setable range surrounding the target, cloning primers at a fixed location, or sequencing primers in an adjustable interval.
  • Primer picking parameters are highly adjustable and primer features can also be accessed after import.
  • For ordering, primers can be exported in csv file format which is commonly used.
  • Bacterial Genome Assembly:
  • Aligner 6 add the option to create fast and memory efficient bacterial genome assemblies.
  • Aligner's scaffolding algorithm generates accurate scaffolds with high coverage.

New in CodonCode Aligner 6.0.0 Beta 2 (Jul 6, 2015)

  • Bug fixes and Improvements:
  • Fixed a bug in scaffolding that caused scaffolds to remain small
  • Scaffolding failed on 32-bit Windows - fixed
  • Known Issues:
  • Updating contigs in roundtrip editing fails if any of the samples or contigs has unaligned ends; to avoid this problem, use ClustalW to generate the contigs for roundtrip editing
  • Aliases (shortcuts) to files do sometimes not work properly, for example when selecting multiple files
  • In the PDF version of the documentation, many bookmarks in the text are slightly wrong - clicking on a link in the text will move to the page just before the correct page
  • File names with special characters may cause problems when imported using "Import -> Add Folder" on Windows (they can be imported using "Import -> Add Samples")
  • On Windows, going to the menu without selecting anything can result in the keyboard being ignored in Aligner (due to a Java bug); if this happens, just click any open Aligner window to select something
  • The actual shortcuts are "space" and "shift-space".

New in CodonCode Aligner 6.0.0 Beta 1 (Jul 6, 2015)

  • New Features and Improvements:
  • Primer picking with Primer3
  • Support for bacterial genome assembly with SparseAssembler
  • Scaffolding of NGS contigs using mate pair information

New in CodonCode Aligner 5.1.5 (Jul 6, 2015)

  • Bug fixes and improvements:
  • Improved accuracy in methylation analysis
  • Adding new sequences to alignments sometimes resulted in bad offsets - fixed
  • When reading SAM files, pair information was not always handled correctly - fixed
  • Fixed a problem where the sample order was wrong when printing contig views

New in CodonCode Aligner 5.1.4 (Jul 6, 2015)

  • Bug fixes and improvements:
  • Better detection of end overlaps between large contigs when assembling
  • Comparing contigs with Clustal or Muscle failed in rare instances - fixed
  • Fixed a problem where methylation analysis failed for some ABI files

New in CodonCode Aligner 5.1.3 (Jul 6, 2015)

  • Bug fixes and improvements:
  • Updated web address used for BLAST searches

New in CodonCode Aligner 5.1.2 (Jul 6, 2015)

  • Bug fixes and improvements:
  • Double-clicking on Aligner project files on Windows works again
  • Improved methylation analysis accuracy by subtracting background
  • Changed format for methylation analysis tags to show background subtracted

New in CodonCode Aligner 5.1.1 (Nov 1, 2014)

  • Added functions to create Bowtie2 alignments and display paired end reads.
  • Additional new features include moving multiple gaps with drag & drop, alignments with Clustal Omega, contig overview printing, and multiple speed and memory improvements for large projects and alignments.

New in CodonCode Aligner 5.0.2 (Jun 12, 2014)

  • fixes several bugs
  • adds improved amino acid translation for codons with ambiguities.

New in CodonCode Aligner 5.0.1 (Mar 28, 2014)

  • CodonCode Aligner version 5.0.1 can create Bowtie2 alignments and display paired end reads. Additional new features include moving multiple gaps with drag & drop, alignments with Clustal Omega, contig overview printing, and multiple speed and memory improvements for large projects and alignments.
  • Bowtie2 Alignments:
  • In CodonCode Aligner you can now align your sequencing data with Bowtie2.
  • Displaying Paired Ends:
  • Paired ends can be dislpayed for Bowtie2 alignments. They are shown in the contig overview and mate information for a read can be found in mouse overs.
  • Improved gap movement:
  • Editing sample and contig gaps just got easier: You can now move more than one gap at the same time in CodonCode Aligner.
  • Aligner' s contig view allows you to use drag and drop to move the gaps and gives instant visual feedback of the gap movement.
  • Print the Contig Overview:
  • Print the contig overview to get a clearly arranged version of your contig and its samples. The overview can be printed for a certain region of your assembly or for the whole contig.
  • Alignments with Clustal Omega:
  • Create alignments with Clustal Omega in CodonCode Aligner.
  • Speed and Memory Improvements:
  • CodonCode Aligenr version 5 includes many optimizations for big projects and large assemblies and alignments. Results are a reduction in needed memory and Aligner being noticeable faster.

New in CodonCode Aligner 4.2.1 (Jul 19, 2013)

  • Introduces support for 64-bit Windows. On 64-bit versions of Windows, CodonCode Aligner 4.2.1 can now use memory beyond the 1.4 GB limit on 32-bit Windows, up to the available amount of physical memory (RAM).

New in CodonCode Aligner 4.0.3 (Jun 9, 2012)

  • Support for Next Generation Sequencing
  • A new contig overview
  • Building trees for selections
  • Splitting contigs using trees
  • Highlighting sequences with labels
  • Reading and writing new file formats, importing subsets

New in CodonCode Aligner 3.7.1 (Sep 22, 2010)

  • Added the option to replace '-' characters in consensus sequences with 'n', and included a number of important bug fixes.

New in CodonCode Aligner 3.6.1 (Jul 31, 2010)

  • Added the ability to make bases in samples and consensus sequences lower case or upper case. Also new is that tags added to consensus sequences are now preserved when samples are added to a contig.

New in CodonCode Aligner 3.5.6 (Apr 3, 2010)

  • Includes performance improvements for large difference tables and bug fixes.

New in CodonCode Aligner 3.5.4 (Mar 4, 2010)

  • Phylogenetic trees:
  • Build Neighbor-Joining trees for your contigs in CodonCode Aligner. Automatically sort your samples by distance when building a tree. You can use the phylogenetic trees as quality control for a simple way to find unexpected differences between your sequences and expected results. Rebuilding the tree after edits in a contig can help you to verify the changes. Each tree is displayed right next to your samples in the contig view. View your trees with branch lengths that represent the number of changes or see the topolgy only. You can export the phylogenetic trees in Newick format.
  • Contig view zooming:
  • Zoom out to view many sequences and their differences at once. Use highlighting of discrepancies and ambiguities to easily spot preserved regions. Easily identify regions with many differences, then zoom for a closer look. Changing the zoom level directly through the popup menu at the bottom left corner of the aligned bases is fast and easy.
  • Automatically shorten reference sequence after alignments
  • Uncovered reference sequences can now be shortened automaticaly after an alignment in CodonCode Aligner. Choose from clipping the reference sequence to a number of uncovered bases on each side, clipping to the alignment or the exon, or not clipping at all.
  • This new feature allows automatic clipping of very long reference sequences to the region you want to look at. For example, a 100,000 bases long genomic reference sequence can be clipped to single exon regions after an alignment.
  • Mask low coverage regions:
  • Automatically mask consensus bases in regions with low coverage. If the coverage is less than what you specified, CodonCode Aligner can change the consensus base to 'N', 'X', or '-' .
  • Percentage consensus:
  • Include only differences that occur in a specific amount of your sequences by using a percentage consensus when building your assembly.
  • The percentage consensus complements the existing options of quality-based, majority, and inclusive consensus, or using the reference sequence as consensus.
  • Also new is the ability to use different consensus methods for regular contigs (for example a quality-based consensus) and contigs of contigs (for example a percentage-based or inclusive consensus).
  • Set base numbers: Set the base number for bases in samples and contigs. This allows you to set and view base numbers relative to (for example) cloning sites or coding sequences.
  • Automatic name scheme definition for "Assemble & Align by Name": The feature "Assemble in Groups" (by name) now offers the option to automatically define a name scheme for the samples in your project. CodonCode Aligner can guess a name scheme based on the delimiters used in your sample names.
  • Customize toolbars directly through popup menus: Just right-click on the toolbar in each view to customize the toolbars through a popup, adding buttons for features you use often, and removing buttons for features you do not use.
  • Support for bi-directional scrolling: For users of mice that support bi-directional scrolling, like Apple's Magic Mouse, we added the option to change the scrolling axes.
  • Rebuild the consensus: Use the popup menu or the menu item to rebuild the consensus; for example after opening a project with different settings.
  • Speed improvements for projects with many contigs

New in CodonCode Aligner 3.0.1 (Apr 2, 2009)

  • Amino acid translation for all samples
  • Translation based background colors
  • Difference tables
  • Import directly from GenBank
  • Script menu
  • New script commands
  • Import 454 data
  • Create new text sequences
  • Larger projects
  • Faster assemblies
  • Automatic memory use on Windows
  • Improved pen tablet support