Programs
Links to useful freeware or shareware programs for molecular genetic analyses.

Population Genetics
Genalex - Excel macro for population genetic analyses of fragment data.
Spagedi - Spatial Genetic Analyses of fragment data
AFLPsurv - PopGen estimates for AFLP
Structure - Bayesian Clustering/Assignment Tests
IM - Isolation with Migration Coalescent Approach
MEGA - PopGen & Phylogenetics of DNA sequence data [plus basic bioinformatics
DNAsp - PopGen on DNA sequence data

Microbes
MiCa
FastGroup

Phylogenetics
Go to Joe Felsenstein's list [here]