Genotype Phenotype Correlation Tool

We present GePhCorT (Genotype Phenotype Correlation Tool), an algorithm that relies on finding the optimal states of the characters over a phylogeny, and then using randomization testing to assess the significance of the correlation between the genotype and phenotype.

Download

• Clone the repository.

git clone https://github.com/Farhat/gephcort.git

• Enter the directory.

cd gephcort

Dependencies

• Python 2.7
• R
• Redis

Setup

• Install redis by typing the following commands into your terminal.

wget http://download.redis.io/redis-stable.tar.gz
tar xvzf redis-stable.tar.gz
cd redis-stable
make
make install

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• Run the python setup file.

python setup.py install

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• Start the redis server.

redis-server

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• Run the resurrect.R script. The generic command format is:

Rscript resurrect.R <sequence_file> <newick_tree_file> <fasta/phylip> <resurrect_output_file>

To try out the script on the example data, use the following command.

Rscript resurrect.R example/example.phy example/example.newick phylip resurrect_output

You can view the sample output by opening the resurrect_output file.

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• Run the reanimate.py script. The generic command format is:

python reanimate.py -s <seq_file> -t <tree_file> -f <format(fasta/phylip)> -i <phen_iterations> -p <phen_file> -r <ressurect_output_file> -o <output_file> -c <cores>

To try out the script on the example data, use the following command.

python reanimate.py -s example/example.phy -t example/example.newick -f phylip -i 100 -p example/example_phenotype.txt -o gephcort_output -r example/example_resurrect.dat -c 1

You can view the sample output by opening the gephcort_output file.