Enveomics collection

A toolbox for microbial genomics and metagenomics

VCF.KaKs.rb

Estimates the Ka/Ks ratio from the SNPs in a VCF file. Ka and Ks are corrected using pseudo-counts, but no corrections for multiple substitutions are applied.

    See source code, Artistic license 2.0.

§ References

    Rodriguez-R & Konstantinidis, 2016, PeerJ Preprints.

§ Requirements

§ Usage

VCF.KaKs.rb --input in_file --seqs in_file [opts]

§ Arguments

Input*
 --input in_file  Input file in Variant Call Format (VCF).
Seqs*
 --seqs in_file  Input gene sequences (nucleotides) in FastA format.
Synonymous fraction
 --syn-frx float  Fraction of synonymous substitutions. If passed, the number of sites are estimated (not counted per gene), speeding up the computation ~10X.
Bacterial code synonymous fraction
 --syn-bacterial-code   Sets the synonymous fraction to 0.760417, approximately the proportion of synonymous substitutions in the bacterial code.
Codon file
 --codon-file out_file  Output file including the codons of substitution variants.
* Mandatory.