PHYLIP

Joe Felsenstein's PHYLIP is a free package of programs for inferring phylogenies. It is the reference all other programs are compared to.

Applications

ProtPars

Generates a phylogenetic tree from protein sequence alignment data using parsimony criteria. The module Bio::Tools::Run::Phylo::Phylip::ProtPars can be used to run this application.

ProtDist

Generates a pairwise sequence distance matrix based on an alignment of protein sequences. Several models of sequence distance can be used including Kimura. The Bio::Tools::Run::Phylo::Phylip::ProtDist module can be used to run this application. A phylogenetic tree can be created from the output from this distance using the Neighbor. The distance matrix produced by this program is parsed with the Bio::Matrix::IO module specifically the Bio::Matrix::IO::phylip which produces a Bio::Matrix::PhylipDist matrix.

SeqBoot

Generate set of series of bootstrap replicate dataset replicates via subsampling with replacements. This can be run with Bio::Tools::Run::Phylo::Phylip::SeqBoot module.

Consense

Calculate a consensus tree typically for a set of bootstrapped replicates. Use the Bio::Tools::Run::Phylo::Phylip::Consense program.

Neighbor

The Neighbor application is used to calculate a phylogenetic tree using either the Neighbor-Joining or UPGMA methods. The input is a pairwise distance matrix typically produced by ProtDist. The Bio::Tools::Run::Phylo::Phylip::Neighbor module can be used to run this program.

Remote execution of PHYLIP

There is also support for running PHYLIP applications remotely through PISE.