Description

PHYLIP (PHYlogeny Inference Package) is a package of programs for inferring phylogenies (evolutionary trees). Methods that are available in the package include parsimony, distance matrix, and likelihood methods, including bootstrapping and consensus trees. Data types that can be handled include molecular sequences, gene frequencies, restriction sites and fragments, distance matrices, and discrete characters.

PHYLIP was developed at the University of Washington. PHYLIP website.

PHYLIP is a single-threaded program, and is intended to be used interactively on helix. The PHYLIP package consists of a large number of individual programs. They are installed in /usr/local/phylip/exe. List of PHYLIP programs.

To run a PHYLIP program, log on to helix.nih.gov using ssh. Then type the name of the program.

Version

The version of Phylip is displayed when any Phylip program is run.

Sample session

% /usr/local/phylip/exe/dnapars
dnapars: can't find input file "infile"
Please enter a new file name> seq

DNA parsimony algorithm, version 3.65

Setting for this run:
  U                 Search for best tree?  Yes
  S                        Search option?  More thorough search
  V              Number of trees to save?  10000
  J   Randomize input order of sequences?  No. Use input order
  O                        Outgroup root?  No, use as outgroup species  1
  T              Use Threshold parsimony?  No, use ordinary parsimony
  N           Use Transversion parsimony?  No, count all steps
  W                       Sites weighted?  No
  M           Analyze multiple data sets?  No
  I          Input sequences interleaved?  Yes
  0   Terminal type (IBM PC, ANSI, none)?  ANSI
  1    Print out the data at start of run  No
  2  Print indications of progress of run  Yes
  3                        Print out tree  Yes
  4          Print out steps in each site  No
  5  Print sequences at all nodes of tree  No
  6       Write out trees onto tree file?  Yes

  Y to accept these or type the letter for one to change
Y
Adding species:
   1. Archaeopt 
   2. Hesperorni
   3. Baluchithe
   4. B. virgini
   5. Brontosaur
   6. B.subtilis

Doing global rearrangements on all trees tied for best
  !-----------!
   ...........
   ...........

Collapsing best trees
Output written to file "outfile"
Tree also written onto file "outtree"
Done.

% ls
outfile  outtree  seq
% cat outfile

DNA parsimony algorithm, version 3.65

One most parsimonious tree found:

                +---------------B.subtilis
  +-------------4  
  |             +----------Brontosaur
  |  
  |                      +-B. virgini
  |        +-------------3  
  1--------2             +------Baluchithe
  |        |  
  |        +-----------Hesperorni
  |  
  +-----------Archaeopt 

requires a total of     21.000

  between      and       length
  -------      ---       ------
     1           4       0.230769
     4      B.subtilis   0.269231
     4      Brontosaur   0.192308
     1           2       0.153846
     2           3       0.230769
     3      B. virgini   0.038462
     3      Baluchithe   0.115385
     2      Hesperorni   0.192308
     1      Archaeopt    0.192308

setenv PATH /usr/local/phylip/exe:$PATH (csh or tcsh)
PATH=/usr/local/phylip/exe:$PATH; export PATH (bash)

Documentation

A primer to phylogenetic analysis using PHYLIP, by Jarno Tuimala. (PDF)
Documentation for all PHYLIP programs