23
Jul
2010
dhinkle9

PHYLIP

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.

Documentation: 

There is extensive documentation available on the web. Information on DNA substitution models is available locally. To learn more about the PHYLIP package go to the PHYLIP home page.

Jarno Tuimala's manual for the use of PHYLIP on molecular sequence data may also be helpful.

Input Format: 
Instructions for All: 

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