Hi all the community! I explain what I need to do.
I actually have 2 files containing a set of genes sequences corresponding of 2 differentes species and what I need to do is to know between all those sequences, which are orthologous to be able to compare each pair of sequence (dN and dS).
Here is a hypotetical exemple of my file:
File 1 :
>seqB (real name is seq 1) AAAACCCCGGGGTTTTT >seqE (real name is seq 2) ACCGGTTGACGGATGGAG >seqC (real name is seq 3) AGGATTAGGATTAGGAAT
>seqC (real name is seq 1) AGGACTAGGATTAGGAAA >seqE (real name is seq 2) ACGGGTTGACGGACGGAG >seqB (real name is seq 3) AAAACCGCGGGGTTTAT
of course, none of those sequences has the same name.
And what I would like to do is to know which of them are orthologous, for exemple a file giving:
Orthologous genes between sp1 : sp2 seq1 : seq3 seq2 : seq2 seq3 : seq1
Thank you very much for you help.