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ka_ks_pipe

Its called ka_ks_pipe, but this is pretty much just a python wrapper to run codeml on a set of genes.

Download and install

I am sharing some precompiled binaries for codeml and muscle. I believe these should work on most systems. If not please install yourself.

Copy the github repository

git clone XXX/ka_ks_pipe.git .

Create conda environment with necessary packages

conda create -n ka_ks_pipe environment.yaml

Activate environment

conda activate ka_ks_pipe

Run the test data

cd ka_ks_pipe/example

python ../bin/ka_ks_pipe --a tmp_a --b tmp_b --output tmp_a.tmp_b.ka_ks.txt

This example should complete within 15 minutes on a single thread

To run with your own data, be sure the following files exist

${genome_a}.cds ${genome_a}.pep ${genome_b}.cds ${genome_b}.pep ${genome_a}.${genome_b}.trans.txt