Free Software

Free software for computational biology.

• Free Software
  • Sequence analysis software projects hosted on this site
    • Visualization
    • Probabilistic sequence modeling
    • Format conversion
  • Other recommended bioinformatics software
    • Sequence alignment & homology search
    • Likelihood phylogeny
    • RNA structure
  • Collaborative media software
  • License

Sequence analysis software projects hosted on this site

Biowiki is the primary documentation site for the following software...

Visualization

• JBrowse: AJAX genome browser
• BubblePlots for rate matrices
• PhyloFilm code & movie archive

Probabilistic sequence modeling

• DART library - includes
  • HandAlign (phylo-alignment/ancestral reconstruction of DNA and proteins)
    • phylocomposer and phylodirector (analysis & visualization of string transducers)
  • xrate (mutation rate measurement, alignment annotation)
    • xfold, xprot and xgram (various xrate presets)
  • stemloc and EvolDeeds (RNA multiple alignment, structure prediction, ancestral reconstruction)
  • simgenome (simulation of genome sequence alignments; requires GSimulator)

• GSIMULATOR (simulation of aligned neutral DNA using string transducers)

Format conversion

• Perl scripts for bouncing around various flatfile formats:
  • GffTools (GFF format: genome features)
  • StockholmTools (Stockholm format: annotated multiple alignment databases)

Other recommended bioinformatics software

Here are some software tools I use frequently (IanHolmes 10/3/06)

Sequence alignment & homology search

• Exonerate (fast, flexible alternative to Genewise, BLAST, BLAT)
• hmmer/Pfam (hidden Markov models of protein families)
• MAVID/MERCATOR (constrained multi-genome alignment)

Likelihood phylogeny

• weighbor (weighted neighbor-joining)
• PAML
• PHYLIP
• MrBayes

RNA structure

• Vienna (RNA folding and kinetics)
• Infernal/Rfam (covariance modeling of RNA families)
• Dynalign (RNA alignment and structure prediction; c.f. stemloc)

Collaborative media software

• TWiki - an open source, hackable Perl wiki engine
  • LinkingToBiologicalDatabases and other TWikiHacks
• WordPress - open source blogware
  • Scoop and Drupal are also highly-rated by many, though I have not used them (except as a client) - IH

License

All software developed in the Holmes lab is released under an open source license.

Except where another license is explicitly specified, this should be taken to be the GNU Public License.