jinhao94 / dnds

Calculate dN/dS ratio precisely (Ka/Ks) using a codon-by-codon counting method.

dN/dS Calculator

Calculate dN/dS ratio precisely (Ka/Ks) using a codon-by-codon counting method. Also calculates the pN/pS ratio precisely (previously referred to as dN/dS).

Usage

>>> sequence_1 = "ATGCTTTTGAAATCG"
>>> sequence_2 = "ATGCGTTCGAAGTCG"
>>> pnps(sequence_1, sequence2)
Fraction(38, 71)
>>> round(float(pnps(sequence_1, sequence2)), 3)
0.535
>>> round(dnds(sequence_1, sequence_2), 3)
0.467