ALISTAT - Simple Alignment Statistics

FMALIGN - Multiple alignment of protein sequences

MOTIFS - Identify Motifs from a set of sequence or alignment

Phylip-Consense - Consensus tree program from Phylip

Phylip-Kitsch - Fitch: Margoliash and Least Squares Methods with Evolutionary Clock

Phylip-Neighbor - Neighbor: Joining and UPGMA methods

Phylip-Proml - Protein Maximum Likelihood program

Phylip-Promlk - Protein maximum likelihood program with molecular clock

Phylip-Protdist - Program to compute distance matrix from protein sequences

Phylip-Protpars - Protein Sequence Parsimony Method

Phylip-Seqboot - a general bootstrapping and data set translation tool

RaxML - Randomized Axelerated Maximum Likelihood

Super - Calculate RMS Deviation between 2 structures