Hello,

I am looking for a way to change the length of the residues printed in the output of trimAl.

Using clustalo, I have generated .aln data that looks like so:

chr1_38402816-38409352                     ---------------------------------------------------------------------------------agatcatgaacttttgctc--ca---agaactattgcaggaa-cataccagga-aagccgagagaatccacagaccctttgaaggaagtggatt
chr1_41176265-41182362                     -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
chr1_42059276-42065372                     -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

I was able to see 175 residues per line by using the --wrap argument in clustalo:

clustalo --in=subsub.noline.fa --out=subsub.noline.aln --force --outfmt=clustal --wrap=175 --threads=6 --verbose

Now I am trimming regions using trimAl, and the output looks like this, with the standard 60 bp length:

chr1_440936-447357                        gggactggtcagtgggt-------------gg-tgtgaagtgccccctagag-------g
chr1_675912-682333                        gggactggtcagtgggt-------------gg-tgtgaagtgccccctagag-------g
chr1_25506586-25512707                    ggaacagcttacagctccagaagacgggtgatttctgaggta-tcactagagtgcca-gg

So, I'm wondering if trimAl has something like "wrap". I have searched the documentation and the supplementary documentation and can't find an answer, although I am new to this so I might have just missed it. Surely it is coded somewhere! Any help would be greatly appreciated.

TIA!