Hello everyone. I have read some papers on Ka/Ks calculations. They said: first all the protein coding genes shold be extracted then Ka/Ks ratio may be calculated by Ka/Ks calculator.

I have 27 new sequenced chloroplast genomes and I think I should align these 27 species and extract all protein coding genes with Geneious software, export that extractions as a fasta format. Then calculate Ka/Ks ratios with Ka/Ks calculator.

But, how can I compare them, I mean should I compare that species one by one. Overal, more than 200 versions may appear. I think I am missing a step in the action, so I have a misunderstanding with it. This is my first independent attemp to do it.

Can anyone help me, please!