Phylogenetic Software
Below is a list of links to various freeware for molecular analyses and phylogenetic inference:
MEGA: Molecular Evolutionary Genetics Analysis (Windows only)
PHYLIP: PHYLogeny Inference Package (Windows, Mac, Linux)
eBiotools (numerous molecular tools in one package; Mac OS X only)
MrBayes (Bayesian inference of phylogeny; Windows, Mac, Unix)
FastPCR (PCR primer design and DNA and protein tools, including in silico PCR; Windows only)