I'm at the stage of trimming my codon sequences for codeml and I want to trim it using Trimal.
However, I can't find any option in trimal to indicate the format of the sequences. Alternatively, Trimal can align for protein sequences, but there is no option to get which sites were trimmed out, which I could use to trim my corresponding nucleotide sequences.
I have also considered using Guidance, but it is much slower and the names were changed.
Please, any help on this?