Phylogenetic analysis

Some of the programs I use most frequently:

Paup* (notes & batch files & manuals)

Mr.Bayes (notes & batch files & manuals)

Mesquite (notes & manual) CURSO MESQUITE

Python

BEAST

BEST (notes & articles)

RaxML (Blackbox) example partition file

T-Coffee Computing, Evaluating and Manipulating Multiple Alignments of DNA, Proteins and Structures

Bioedit

MEGA

DAMBE

jModelTest

Also useful (software lists & online computing services):

CIPRES Cyberinfrastructure for Phylogenetic Research

CBSU Web Computing Interface

EMBL European Molecular Biology Laboratory

European Bioinformatics Institute

Felsenstein's Phylogeny Program portal

Oslo Bioportal