Introduction

PHYLIP (PHYLogeny Inference Package) is a package of programs for inferring phylogenies (evolutionary trees). It is maintained and developed by Dr. Joe Felsenstein at University of Washington. Methods that are available in the PHYLIP package include DNA and protein parsimony, distance matrix, and likelihood methods, including bootstrapping and consensus trees.

Features

The SGI optimized and parallelized PHYLIP package has been installed on Helix Systems. The most time consuming PHYLIP algorithms, dnaml, dnamlk, dnapars, and protpars, have been optimized for SGI systems and the protpars method has also been parallelized for SGI systems.

Benchmark

This graph is produced by Helix Systems based on running 200 GPCRs using parallelized PROTPARS with increasing number of processors. The data point at 0 is produced from original non-SGI optimized version of protpars.

Website

http://evolution.genetics.washington.edu/phylip.html

User Guide

http://evolution.genetics.washington.edu/phylip/phylip.html

Sample Session

1. See the sample file at the end of this page.

2. To initialize phylip package, type 'phylip' at the command prompt

<helix> % phylip
---------------------------------------------------------------------------
PHYLIP v3.573 on Helix Systems
---------------------------------------------------------------------------
Please type the program name and required arguments to start
Go to http://evolution.genetics.washington.edu/phylip/phylip.html for help

3. Go to the directory where your input file is located. Rename your input file to 'infile'. Type the program name. Please note, if you didn't rename your input file to 'infile', an error message will show up and prompt you for a new file name. Go ahead and type in the correct file name and path if needed.

<helix> % protpars
./protpars_mp.sgi: can't read infile
Please enter a new filename> /data/user/filename

Protein 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) Y

4. Two files will be created: 'outfile' and 'treefile'.

5. Sample file:

8 110
chiins BALWIRSLPL LALLVFSGPG TSYAAANQHL CGSHLVEALY LVCGERGFFY
xenins BALWMQCLPL VLVLFFSTPN TE-ALVNQHL CGSHLVEALY LVCGDRGFFY
humins BALWMRLLPL LALLALWGPD PAAAFVNQHL CGSHLVEALY LVCGERGFFY
monins BALWMRLLPL LALLALWGPD PVPAFVNQHL CGSHLVEALY LVCGERGFFY
dogins MALWMRLLPL LALLALWAPA PTRAFVNQHL CGSHLVEALY LVCGERGFFY
hamins MTLWMRLLPL LTLLVLWEPN PAQAFVNQHL CGSHLVEALY LVCGERGFFY
bovins MALWTRLRPL LALLALWPPP PARAFVNQHL CGSHLVEALY LVCGERGFFY
guiins MALWMHLLTV LALLALWGPN TGQAFVSRHL CGSNLVETLY SVCQDDGFFY

SPKARRDVEQ PLVSS---PL RGEAGVLPFQ QEEYEKVKRG IVEQCCHNTC
YPKVKRDMEQ ALVSG---PQ DNELDGMQLQ PQEYQKMKRG IVEQCCHSTC
TPKTRREAED LQVGQVELGG GPGAGSLQPL ALEGSLQKRG IVEQCCTSIC
TPKTRREAED PQVGQVELGG GPGAGSLQPL ALEGSLQKRG IVEQCCTSIC
TPKARREVED LQVRDVELAG APGEGGLQPL ALEGALQKRG IVEQCCTSIC
TPKSRRGVED PQVAQLELGG GPGADDLQTL ALEVAQQKRG IVDQCCTSIC
TPKARREVEG PQVGALELAG GPGAGG---- -LEGPPQKRG IVEQCCASVC
IPKDRRELED PQVEQTELGM GLGAGGLQPL ALEMALQKRG IVDQCCTGTC

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