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/