The phyogenetics software section of this web site contains information on software used for either various phylogenetic analysis
Software pages are available for the following programs:
Clustal W
Clustal X
FASTA
MAFFT
SeaView
Are We There Yet? (AWTY)
BEAST
BEAUti
DataMonkey and HyPhy
FigTree
GARLI
Genealogical Sorting Index (gsi)
jModelTest
ModelTest
MrBayes
PAML
PAUP*
PHYLIP
Phycas
Tracer
TreeStat
LAMARC
MIGRATE-N
Structurama