Phylip - a collection of programs for phylogenetic inference

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Phylip, the "phylogenetic inference package", is a collection of command line programs for inferring evolutionary trees from sequence and other data. Phylip is distributed as a free program suite by Dr. Joe Felsenstein at the University fo Washington, Seattle.

The Phylip home page - the ultimate source for documentation and infomration. The package may also be downloaded - pre-compiled versions are available for OS X and Windows. Source code is available to compile on other platforms.

ACHS has Phylip (ver. 3.66) installed on the GCG server, watson.achs.virginia.edu. Phylip programs runs at the command line under the GCG shell. Simple login to watson.achs.virginia.edu, start a GCG session by typing "gcg", then run your Phylip commands from the >GCG> shell prompt.

Some of the programs in Phylip are also available to be run from web sites, such as the Institute Pasteur, and the University of Hong Kong. Check these web sites carefully to be sure you are of just what version of gcg you are running.

Tutorials and Handouts

PHYLIP documentation On-line documentation of all PHYLIP commands (also available here or here,)

Introduction to PHYLIP A tutorial that provides an introduction to using PHYLIP as well as practical examples of how to format sequences and run the programs (on-line tutorials are also available - check the listings at the "Phylip on the Web" page ).

Other Programs and Utilities

Readseq is a utility program that will convert GCG's msf format files to PHYLIP format (conversion can also be done through web servers such as at Indiana University and Baylor College of Medicine). The conversion is not perfect, so see the "Introduction to PHYLIP" tutorial for details.

Links to other phylogenetic programs. These sites are a useful resource to see what other programs are available. We cannot possibly maintain and support all the programs that are available

Running PHYLIP jobs in the background on watson.achs.virginia.edu

Ordinarily, PHYLIP programs are run in the foreground by executing them at a >GCG> prompt (ie. starting gcg first to initialize the gcg shell). As taken from the "Main" PHYLIP documentation, programs can be run in the background by altering the input file to include the responses to a program's pre-run interactive menu:

"For example: suppose you want to run DNAPARS in a background, taking its
input data from a file called sequences.dat, putting its interactive output to
file called "screenout", and using a file called "input" as the place to store
the interactive input. The file "input" need only contain two lines:

sequences.dat
Y

which is what you would have typed to run the program interactively, in
response to the program's request for an input file name if it did not find a
file named "infile", in in response the the menu.

To run the program in background, you would simply give the command:

dnapars < input > screenout &

which runs the program with input responses coming from "input" and interactive
output being put into file "screenout". The usual output file and tree file
will also be created by this run (keep that in mind as if you run any other
PHYLIP program from the same directory while this one is running in background
you may overwrite the output file from one program with that from the other!)."

Just create a text file that includes the actual data input file name as the first line, then the menu responses, each on a separate line, and execute this text file as shown above. For example, executing "dnapars" at the >GCG> prompt would normally bring up the following screen:

DNA parsimony algorithm, version 3.573c

Setting for this run:
U Search for best tree? Yes
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
M Analyze multiple data sets? No
I Input sequences interleaved? Yes
0 Terminal type (IBM PC, VT52, ANSI)? 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

Are these settings correct? (type Y or the letter for one to change)

Your input text file for background execution needs to include any response to these settings, in order, one per line. Note that some responses require multiple lines to respond (run the program interactively to see what your responses will need to be). So the following in a text file named input:

sequence1.dat
J
32217
10
2
Y

would be used (in the command line dnapars < input > sequence1.out &) to start the program dnapars, use the file sequence1.dat as the infile (ie. the data file), turn on the Jumble option, provide it with a random seed (eg. 32217), run 10 iterations of the jumble option, turn off the progress run indications, and now start the program (your file will always end with a "Y"). Once the command is initiated, the user can exit GCG, logoff of watson, and their PHYLIP job will run in the background until complete.

Local Support
Further user support, such as personal instruction and cooperative projects with a faculty member, is available. Contact mblack@virginia.edu.

Please email comments or suggestions about the ACHS MolBiol pages to mblack@virginia.edu.

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