Leigh Brown

Useful software for Viral Evolution

Sequence alignment

BioEdit (quite old but useful)
Geneious (does a lot, new)

Tree & evolutionary software

Mega 5 (NJ and ML trees, fast)
HyPhy (Datamonkey webserver, standalone software also available)
MrBayes (Bayesian Tree inference)
BEAST (Coalescent based bayesian tree inference, need BEAUTi to set it up)

Tree viewing and utilities

FigTree (use with any tree, but especially BEAST trees)
Tracer (use to analyse some of the BEAST results)

Statistical Software & Programming

R also packages seqinr, ape and statnet
Java - Eclipse