Steps for trimming aligned peptides using Trimal

Question

I am trimming the aligned peptide sequences and back transleting them to codon using Trimal.

Here i am using following cmd's: /mnt/genome3/Lab_Users/Kishor/DISK_2/softwares/trimal-1.4.1/source/trimal -in OG0008206.fa.aln.out -out OG0008206.fa.aln.out_1st.trim -automated1 -backtrans OG0008206.fa.codon

/trimal-1.4.1/source/trimal -in OG0008206.fa.aln.out_1st.trim -out OG0008206.fa.aln.out_2nd.trim -phylip_paml -nogaps

But i am confused about, should i remove the gaps fisrt and then backtransleted the peptides or Backtransleted first and then remove the gaps. Because i am getting different results (codon) in two attempts. which one i should do fisrt? Thanks.

Answer 1

I would try an alternative package. Transalign is the traditional package, albeit old now. There's fairly large published record since. Also check out stackoverflow's response, here

You can write your own script. I wrote mine based-around Blast.