Geneious Pro is an integrated bioinformatics tool suite for manipulating, sharing, finding and exploring biological data such as DNA sequences or proteins, 3D structure information, phylogenies, publications, etc.

Geneious Pro features sequence alignment and phylogenetic analysis, contig assembly, primer design and restriction analysis, access to biological databases, BLAST, protein structure viewing, NCBI, EMBL, PubMed auto-find, and more. It even includes an API for creating your own plugins.

Geneious provides sophisticated genome & proteome research tools, protein or molecular visualization, publication literature search and storage tools and more, with revolutionary usability.

So you get more done. And faster results � faster to publication or faster to discovery.

Here are just some examples of everyday research work that Geneious Pro can do for you.

￭ Sequence Analysis:Consensus sequence, translation and complement update as you edit
Several pairwise and multiple sequence alignment options including Progressive pairwise and alignment of nucleotide translation
Phylogenetic tree building with UPGMA, NJ with bootstrapping and consensus trees
User-friendly plugin to MrBayes bayesian analysis
Print trees for insert into your research, preserving tree-lengths.
Find open reading frames (ORFs)

￭ Sequence Visualization:
Customizable graphical viewer and editor of sequences, alignments and annotations
Interactive phylogenetic tree viewer with fast selection of source sequences in alignment
Graphs updated real-time including sequence logos, chromatogram traces and protein properties
3D protein structure viewing
Fast, interactive dot plots

￭ Lab End Sequence Analysis
Contig assembly with automated trimming, assembly, and chromatogram editing
Restriction enzyme mapping and digestion
Design primers with ambiguities and mismatches
Test individual primers or search a set of primers for the best matches

￭ Organize sequences and publications in a database
Store and organize all of your research material in one place
Search and sort sequences by similarity, basic and advanced text searching of data
Extensive import and export including Endnote, Nexus, Newick, Fasta, PDF, ABI and many more!
Add your own custom notes to sequences, alignments and trees.

￭ Download protein sequences and gene sequences:
Drag and drop sequences from NCBI (including Gene, Genome, Nucleotide, SNP, Structure and Protein)
Close integration with Pfam databases
Keeps your NCBI and EMBL downloads up to date automatically
NCBI BLAST sequences with two clicks of the mouse
A unique method of rapidly filtering public data as it downloads.

￭ Teach Bioinformatics
Create interactive tutorials with direct links to material in Genieous
All the tools a budding bioinformatician may need is just a click away
Students can answer question, do analyses then submit their results using Collaboration

￭ PubMed search:
Automatically retrieves newly published articles and can sort them based on your interests
Storage of abstracts and bibliographic information
Quick links to find original articles and citation record online.

Here are some key features of "Geneious Pro":

￭ Collaborate � Share documents and chat with other users of Geneious Pro from anywhere in the world
￭ Contig assembly � Automated contig assembly, sequence trimming and easy contig editing
￭ Sequence viewing � Circular sequence viewer. Consensus, translation and complement along-side sequences.
￭ Sequence editing � Edit sequences, sequence alignments and annotations
￭ Primers � designing and testing with ambiguities, mismatches and multiple primer searching. (This product includes software developed by the Whitehead Institute for Biomedical Research)
￭ Restriction analysis � Find and view restriction cut sites and perform restriction enzyme digests
￭ Agents and smart agents � Agents keep your data up to date while smart agents learn about the documents you are interested in and find more for you!
￭ Sequence graphs � Sequence logo graph, view and edit chromatogram sequences.
￭ Extended connectivity � Create custom BLAST databases. Seamless integration with Pfam, NCBI Gene and NCBI SNP databases.
￭ Advanced alignment � ClustalW alignment, translation aignment and profile alignment (alignment to alignment and sequence to alignment)
￭ Geneious education � Create and use interactive tutorials for learning within Geneious
￭ Interoperability � Import formats from other tools like DNAStar, PIR, EMBL, GCG and Phylip
￭ Chromosome viewing � Load, view, edit full human chromosomes or up to 10,000 HIV genomes
￭ Publication images � Publication quality image export to vector graphic formats
￭ Organize and visualize � Organize, visualize and search sequences (with annotations), alignments, phylogenetic trees, publications, protein structures and more!
￭ Database integration � Seamlessly integrated searching with Genbank, PubMed, BLAST and UniProt
￭ Align and build trees � Basic pairwise alignment, multiple alignment and tree building methods including bootstrapping and consensus trees.
￭ Import and Export � Import and export Newick, Nexus, FASTA and Endnote formats. Import PDF, 3D Structures, .rsf, .msf, Chromatograms, DNA Strider, Clustal
￭ Plugins � Public Java API (application programming interface) for developing your own plugins
￭ Annotation Viewing - Labels are positioned intelligently outside of region markers at low zoom
￭ Quality information is now imported from .ace files if available
￭ Chromatogram quality values are displayed in the Text View
￭ Save As... (Ctrl+Shift+S) added to File menu
￭ Protein structures now display all amino acid and DNA sequences
￭ New sample documents
￭ PopSet results now downloaded in sets
￭ Added more annotation types with improved coloring
￭ Annotations downloaded from GenBank are given more informative names

Requirements:

· Java 1.5 or 1.6, included in the installer

Limitations:

· 14 days trial

What's New in This Release: [ read full changelog ]

· New features added in Pro version only:
· Cloning operation - Insert into vector provides one-step insertion into a plasmid
· Plasmid maps - restriction sites and annotations on circular sequences are now shown with the label pointing to the region
· Tree coloring - branches and labels can now be colored in the Tree View
· DeCypher - Added support for searching using TimeLogic's DeCypher accelerator hardware