[BiO BB] Ka/Ks

[Peter Groenen]

I am looking for a command line tool that can handle protein alignments as input and aligns the corresponding transcripts. I want to use it for Ka/Ks determination.
Secondly, I need something like a "sliding " Ka/Ks determination to see if there is a difference within a protein when looking at smaller segments. 
I looked at SNAP, and also PAML but they are not very straightforward in use, especially hte diffenret formats are giving me trouble.
Any ideas?
Thanks in advance.
Peter
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