Installation Guide of ConcaterPillar and its dependencies

ConcaterPillar is a hierarchical likelihood ratio test for phylogenetic congruence.

Dependences: RaxML, Python, SciPy library and pyMPI.


$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)

First, install dependences by typing:

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

Download the pyMPI:

Uncompress the source and type:

$sudo make
$sudo make install

Installation of ConcaterPillar


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

Type on shell:

$sudo chmod 777

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:


If everything is right you will see this message:

path verified…
installation complete.

Now, run the “”


Copy your input files to concaterpillar directory.

Input files

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

Running ConcaterPillar


$python -a -t -c 1
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