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.
Version on CSC's Servers
The software needs to be initialized before use.
On Taito type:
module load biokit
The programs that form the package can then be invoked by their names. For example:
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.
If you are doing an analysis that takes long time, it may be reasonable to build a command script file that can be executed as a batch job in Taito.
Here's an example of a PHYLIP command script file for bootstrapping using distance methods.
#!/bin/bash # 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 # 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
You can save this script as e.g. phylip.job.sh and the make it executable:
chmod u+x phylip.job.sh
You can now construct a Taito batch job file:
#!/bin/bash -l #SBATCH -J phylip #SBATCH -o output_%j.txt #SBATCH -e errors_%j.txt #SBATCH -t 10:00:00 #SBATCH -n 1 #SBATCH --mem-per-cpu=4000 # module load biokit ./phylip.job.sh
to submit the job to the queue use:
See Taito user guide for details.
DrawTree and DrawGram
To use DrawTree and DrawGram you need font files. These are provided with the software, but the programs try to look for them in your current directory, not in the installation folder. The easiest way to use them is to copy them into your own folder:
cp /homeappl/appl_taito/bio/phylip/phylip-3.695/exe/font* .
The programs look for a file called "fontfile" by default, so if you have a favorite font, you can copy it by that name, e.g.
cp font1 fontfile
Alternatively you can just provide a full path name to a font file when prompted.
More information can be found on the PHYLIP home page.