ConcaterPillar

Concaterpillar

Installation Guide of ConcaterPillar and its dependencies

ConcaterPillar is a hierarchical likelihood ratio test for phylogenetic congruence.

Dependences: RaxML, Python, SciPy library and pyMPI.

RaxML

$sudo apt-get install raxml

SciPy library

For linux users, just type on shell:

$sudo apt-get install python-numpy python-scipy python-matplotlib ipython ipython-notebook python-pandas python-sympy python-nose

pyMPI (In case of using more than one processor)

http://pympi.sourceforge.net/index.html

First, install dependences by typing:

$sudo apt-get install build-essential
$sudo apt-get install python-dev libopenmpi-dev

Download the pyMPI: http://sourceforge.net/projects/pympi/

Uncompress the source and type:

$./configure
$sudo make
$sudo make install

Installation of ConcaterPillar

Website:
http://rogerlab.biochemistryandmolecularbiology.dal.ca/Software/Software.htm
http://rogerlab.biochemistryandmolecularbiology.dal.ca/ccp.php

Go to the directory of Concaterpillar and run the script “ccpinstall.py”.
This script should be run to either find or verify the path to RaxML.

Type on shell:

$sudo chmod 777 ccpinstall.py
$python ccpinstall.py

This message will appear:
“No path for raxml is specified, please enter a path, q to quit”

Then, type the directory where the file raxmlHPC was created:

$/usr/bin/raxmlHPC

If everything is right you will see this message:

path verified…
installation complete.

Now, run the “concaterpillar.py”

$python concaterpillar.py

Copy your input files to concaterpillar directory.

Input files

  • amino acid/nucleotide alignments (NEXUS, PHYLIP, FASTA).
  • it must have the extension “.seq”.

Running ConcaterPillar

Type:

$python concaterpillar.py -a -t -c 1
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