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6.0 years ago
mah123
•
0
Anyone familiar with the gKaKs pipeline (Zhang et al. 2013): Can this pipeline use transcriptomic data to calculate Ka/Ks? I assume it does, but it would be nice to have confirmation from somebody familiar with the pipeline. Thanks!
Hi,
As far as I know, gKaKs is synonymous of dN/dS ratio. For dN/Ds analysis, you need coding sequences and their protein sequences to perform the analysis. I have not done gKaKs analysis, but I have done dN/dS. I used mRNAs and their protein sequences and followed: 1. single copy orthologs of species 2.Coding-specific alignment (Pal2aln tool) 3.Codeml tool in PAML package.
I hope this helps.