PHYLIP

Phylip (PHYLogeny Inference Package) is a software package that includes a variety of tools for determining the phylogenetic relationship between sets of related nucleic acid and protein sequence. It also contains tools for visualizing the results of these phylogenies. It has been in development since 1980 and is regularly updated by its creator, Dr. Joseph Felsenstein.

The input for the phylogenetic programs in Phylip package is a file of sequences that have been previously aligned with a tool such as Clustal W and that is in the ‘Phylip format’. The input for the tree drawing programs will be the output from these files (please see flow chart) , many tools have pipelines set up to process the output of a given phylogeny tool such as dnaml to the next logical set of programs one may want to use.