GitHub - popgenomics/pNpSdNdS: pNpSdNdS computes exact synonymous and non-synonymous polymorphism

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pNpSdNdS computes exact synonymous and non-synonymous polymorphism

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README.txt		README.txt
pNpSdNdS.py		pNpSdNdS.py

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Compute piN, piS for an ingroup species using popPhyl's Fasta file.
TODO: dN and dS

ex: ./pNpSdNdS.py Mytilus_galloprovincialis#solo200.cds Mytilus_galloprovincialis provin 
1st argument: infile's name with all sequences in the following format:
>Contig4|Mytilus_galloprovincialis|GA36A|Allele_1
ATGCACAGTANNNACTAGTAG....


2nd argument: name of the ingroup species (Mytilus_galloprovincialis here)

3rd agument: name of the outgroup species (not included yet)




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ex :
./pNpSdNdS.py /home/croux/Documents/manuscript_DILSABC/datasets/silene/assembly/reads_2_snp_v2/silene.fas sp truc