Between '-backtrans' and '-nogaps' parameter, Which one to use first? #63
Description
Hi,
I am using trimal v1.4.rev15 to trim and back-translate into codon to make the alignment suitable fo PAML. Since running it i have found that -automated1, -backtrans, -nogaps can not be run together. So i decieded to remove the gaps first from the peptide alignment and then to the back translation. My cmd lines look like:
/trimal-1.4.1/source/trimal -in OG0008206.fa.aln.out -out OG0008206.fa.aln.out_1st.trim -phylip_paml -nogaps
/mnt/genome3/Lab_Users/Kishor/DISK_2/softwares/trimal-1.4.1/source/trimal -in OG0008206.fa.aln.out_1st.trim -out OG0008206.fa.aln.out_2nd.trim -automated1 -backtrans OG0008206.fa.codon
I also tried in oposite way by backtranleting first and then remove the gap. But i received the two different set of codons(though the nuc/pep number was same).
Can i get any suggestion?
Thanks.