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

Here i am using following cmd's:

trimal -in  OG0008206.fa.aln.out -out OG0008206.fa.aln.out_1st.trim -automated1 -backtrans OG0008206.fa.codon
trimal -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.



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