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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.
Version 3.66
Input data file format
PHYLIP
Instructions
A demonstration of PHYLIP will be given by Joe Felsenstein.
Local documentation is available. There is also 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.
Sample files for the demonstration:
cytb.prt
eftualpha.prt
fifteen.dna
fifteen.dst
hasegawa.dna
primates.dna
mamhbb.prt
mamhbb.dna
mammalspenny.prt
sarich.dst
ten.prt
turbeville.dna
turbeville.wts
The font files (e.g., font1, font2, ...) are present in each user's home directory. These files are needed for drawgram and drawtree.
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