Dear BioStars Users,
I am using KaKs Calculator to estimate selection over a whole sequence, and I need to do this for many multifasta alignments. Here is some example file:
>ref AAAAAAA >seq1 BBBBBBB >ref AAAAAAA >seq2 CCCCCCC >ref AAAAAAA >seq3 DDDDDDD
And here is what I would like to get (an AXT formatted file):
seq1 AAAAAAA BBBBBBB seq2 AAAAAAA CCCCCCC seq3 AAAAAAA DDDDDDD
I already tried this script but it's not doing properly.. Would anyone have a pipeline (in bash, perl, R, python...) to automatize this, or have an idea of how to proceed? I can for sure do it by hand for several files, but I have too many to do it :)
Thanks a lot!