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.