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

• Prototype GBrowse: AJAX interface to the generic genome browser
• Bubble Plots for rate matrices
• Phylo Film code & movie archive

Probabilistic sequence modeling

• DART library - includes
  • Handel (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 evoldoer (RNA multiple alignment, structure prediction)

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 (Ian Holmes 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
• Mr Bayes

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, Scoop - open source blogware

License

All software developed in the Holmes lab is released under the GNU Public License.