Version

PHYLIP Version 3.68 is installed in HIPPU

Description

PHYLIP is a FREE package of programs by Joseph Felsenstein for inferring phylogenies and carrying out certain related tasks. At present it contains 35 programs.

Usage

The program is installed in Hippu (hippu.csc.fi).

The software needs to be initialized before use:

module load phylip

The programs that form the package can then be invoked by their names. For example:

dnapars

The programs read the input file from the current directory. The input file has to be named 'input'. The programs write to the file 'outfile' and/or 'treefile'.

If you are a first time user, start out by reading the relevant parts from the main PHYLIP documentation and then proceed to read the program specific texts below.

Phylip command scrtipts in Hippu.

Hippu does not have a batch jobs sysem and you can run also very large jobs as interactive jobs. However, if you are doing a massive ananlysis that takes long time it may be reasonable to build a commad script file that can be executed as a background jobs. Here's an example of a phylip commnad scriopt file for bootstrapping using distance methods in Hippu. Save the script with a name batch and submit it into run with command source batch.

#!/bin/csh

set alku='date'

# Removes old analysis files
rm -rf outfile
rm -rf outtree
rm -rf intree 
rm -rf infile1
rm -rf infile2
rm -rf infile3 
rm -rf phyout
rm -rf phytreeout

module load phylip

# Resampling phase
seqboot <<EOF
r
10
y
1
EOF

mv infile infile1
mv outfile infile

# Distance calculation phase
dnadist <<EOF
m
d
10
y
EOF

mv infile infile2
mv outfile infile

# Neighbor-joining tree phase
neighbor <<EOF
m
10
3
y
EOF

mv infile infile3
mv outfile infile
mv outtree intree

# Majority rule tree phase
consense <<EOF
y
EOF

mv outfile phyout
mv outtree phytreeout

# The infile will contain the sequence alignment...
mv -f infile1 infile

echo Ajo alkoi: $alku
echo Ajo päättyi: 'date'

Documentation

Documentation can be read online.

Tips and examples

• You can download the executables for DOS and several other platforms from Phylip's homepage.
• A free booklet covering basics of phylogenetic analysis with Phylip using molecular sequences: A primer to phylogenetic analysis using Phylip package.

User support