Easiest way to calculate Ka Ks ratio and divergence time

The Ka/Ks ratio is used to estimate the nature of evolution among neutral, purifying selection and beneficial mutations acting on a set of homologous protein-coding genes. Although there are several wonderful programs out there to calculate the Ka, Ks and Ka/Ks ratio but kaks function of R package seqinr is the easiest way to do it. The function kaks use the method published by Li et al (J. Mol. Evol., 36:96-99, 1993) to calculate the Ka, Ks and Ka/Ks ratio. In the following script take aligned the fasta sequences in the clustal format and, finally, R package seqinr will be used to calculate the Ka, Ks and Ka/Ks ratio.
Cheat Sheet to Install and work with R on Ubuntu HERE


We need the following R libraries to run the script
  • seqinr
  • ape
  • phangorn


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