Bioinformatics Software
Here we present a catalogue of bioinformatics software that is prevalent amongst users at the Colindale site, with brief reviews, information links and, where available, current pricing information. We welcome software recommendations from any of our users, so if you have a product you are impressed with let us know.
Software Reviews
Click on one of the names below to see the review of the product.
Artemis - Go to website
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Description
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Genome scale sequence viewer/annotation tool
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Comments
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- Supports EMBL or Genbank file formats and FASTA sequence data.
- Six frame nucleic acid translation
- Directs links to coding annotation
- User friendly graphical interface
- Straightforward installation with good online documentation.
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Pricing
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Free
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Artemis Comp arison Tool (ACT) - Go to website
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Description
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Genome scale sequence comparison tool
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Comments
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- Allows direct comparison of two or more complete genome sequences.
- Extends functionalitry of Artemis.
- Runs on Linux/ Unix operating systems (does not run successfully on Windows in our experience)
- Working knowledge of Unix needed to install the software.
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Pricing
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Free
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BioEdit - Go to website
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Description
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Sequence alignment, editing and manipulation program
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Comments
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- Very versatile package including alignment, tree generation, restriction mapping and plasmid annotation functions.
- ClustalW based sequence alignment.
- Local and internet BLAST capability.
- User friendly graphical interface.
- Wide range of colouring and presentation options.
- Easily installed from downloaded ZIP file.
- Now updated to be compatible with Win2K and WinXP
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Pricing
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Free
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Bio Numerics - Go to website
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Description
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Biological analysis and database package
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Comments
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- Current staple of HPA bioinformatics.
- Capable of handling many different types of experimental data.
- Good initial analysis capability, particularly with clustering and comparison tools.
- Functional flexibility provided by scripting language.
- Excellent support provided.
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Pricing
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Contact Supplier
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PHYLIP - Go to website
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Description
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Package of several different phylogenetic tools
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Comments
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- Wide range of phylogenetic techniques available
- Non-graphic (command-line) interface
- Good online documentation
- A little difficult for novice users to integrate the various programs to give meaningful results
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Pricing
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Free
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MEGA - Go to website
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Description
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Molecular Evolutionary Genetic Analysis
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Comments
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- Powerful phylogenetic analysis tools built in
- Can perform selection analyses, relative rates tests and calculate complex sequence distance statistics
- Publication quality tree rendering
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Pricing
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Free
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SwissPDB viewer - Go to website
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Description
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Molecular visualisation and analysis tool
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Comments
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- Visualisation of 3D structures from the Protein DataBank (amongst others)
- Very functional, providing basic analysis of single structures and comparisons between pairs of structures.
- Good online and local documentation.
- Easy to install from downloaded archive.
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Pricing
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Free
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Tree view - Go to website
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Description
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Displays phylogenetics relationships (trees)
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Comments
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- Supports a number of file formats including PHYLIP and NEXUS.
- Limited tree editing possible.
- Extremely useful in conjunction with BioEdit.
- Easily installed from downloaded ZIP file.
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Pricing
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Free
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Last reviewed: 13 April 2010
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