How to generate pair-wise alignments for all the orthologous gene pairs at once?

Question

[kashiff007]

Hi everyone,

I want to calculate Ka/Ks value between two organism. For this I have to align pairwise each orthologs. I can align one pair at a time but I need to know how to align each pair at once. I have tabulated blast output which have the headers of each pair.

Please help me for this.

[Biomonika (Noolean)]

Please show an example of how your data look like.