- 1 Free Software
- 1.1 Sequence analysis software projects hosted on this site
- 1.2 Other recommended bioinformatics software
- 1.3 Collaborative media software
- 1.4 License
Free software for computational biology.
Sequence analysis software projects hosted on this site
Biowiki is the primary documentation site for the following software...
Probabilistic sequence modeling
- DART library - includes
- Hand Align (phylo-alignment/ancestral reconstruction of DNA and proteins)
- xrate (mutation rate measurement, alignment annotation)
- stemloc and Evol Deeds (RNA multiple alignment, structure prediction, ancestral reconstruction)
- simgenome (simulation of genome sequence alignments; requires GSimulator)
- GSIMULATOR (simulation of aligned neutral DNA using string transducers)
- Perl scripts for bouncing around various flatfile formats:
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)
- 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
- WordPress - open source blogware
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.