PHYLIP is a set of modular programs for performing numerous types of phylogenetic analysis. Individual programs are broadly grouped into several categories: molecular sequence methods; distance matrix methods; analyses of gene frequencies and continuous characters; discrete characters methods; and tree drawing, consensus, tree editing, tree distances. Together the programs accommodate a broad range of data types including, DNA, RNA, protein, restriction sites, and general data types. The programs encompass a broad variety of analysis types including parsimony, compatibility, distance, invariants and maximum likelihood, and also include both jackknife and bootstrap re-sampling methods. The output from one program often forms the input for other programs within the package (e.g., dnadist generates a distance matrix from a file of DNA sequences, which is then used as input for neighbor to generate a neighbor-joining tree and the tree is then viewed with drawtree). Therefore for a typical analysis the user makes choices regarding each aspect of an analysis and chooses specific programs accordingly. Programs are run interactively via a text-based interface that provides a list of choices and prompts users for input.
PHYLIP sample files
- cytb.prt – Cytochrome B protein sequences
- eftualpha.prt – EFTU Alpha protein sequences
- fifteen.dna – Large subunit rRNA sequences for 15 eukaryotes
- fifteen.dst – A set of distances for the above
- hasegawa.dna – Mitochondrial D-loop and adjacent 3rd positions for apes
- primates.dna – The same, for a wider range of primates
- mamhbb.prt – Mammalian hemoglobin beta sequences
- mamhbb.dna – Mammalian hemoglobin beta DNA sequences
- mammalspenny.prt – David Penny’s concatenation of mammal proteins
- sarich.dst – Immunological distances from Sarich 1969 Syst. Zool.
- ten.prt – COX II protein sequences of mammals
- turbeville.dna – Turbeville et al MBE 1994 large subunit rRNA for chordates
- turbeville.wts – 0/1 weights for the above identifying well-aligned regions