Groups
| Leigh Brown | http://hiv.bio.ed.ac.uk/index.html |
| Rambaut | http://tree.bio.ed.ac.uk |
Useful software for Viral Evolution
Sequence alignment
| BioEdit | http://www.mbio.ncsu.edu/bioedit/bioedit.html | (quite old but useful) |
| Geneious | http://www.geneious.com/ | (does a lot, new) |
Tree & evolutionary software
| Mega 5 | http://www.megasoftware.net/ | (NJ and ML trees, fast) |
| HyPhy | http://www.datamonkey.org/ | (Datamonkey webserver, standalone software also available) |
| MrBayes | http://mrbayes.csit.fsu.edu/ | (Bayesian Tree inference) |
| BEAST | http://beast.bio.ed.ac.uk/Main_Page | (Coalescent based bayesian tree inference, need BEAUTi to set it up) |
Tree viewing and utilities
| FigTree | http://tree.bio.ed.ac.uk/software/figtree/ | (use with any tree, but especially BEAST trees) |
| Tracer | http://tree.bio.ed.ac.uk/software/tracer/ | (use to analyse some of the BEAST results) |
Statistical Software & Programming
| R | http://www.r-project.org/ | also packages seqinr, ape and statnet |
| Java - Eclipse | http://www.eclipse.org/downloads/ |