trimAl doesn't recognise alignment

[honeyella]

Hi,

I have tried to find an answer by searching google but couldn't find anything.
I aligned my Data with mafft and now wanted to trim with TrimAl. The first two sequences worked but then I received following error message:

ERROR: The sequences in the input alignment should be aligned in order to use trimming method.

I will attach the file in question. CoaE.mafft.zip

The command used was:

trimal -in CoaE.mafft -out CoaE.triaml.fasta -fasta - automated1

Thank you for helping.

PS I really do hope this isn't a stupid question.

I have the same issue with some of my protein alignments, but it works fine on the codon alignments.
All were in FASTA format and changing the file extension produced the same results.

trimal -in INPUT -out OUTPUT -gt 0.9

[Yorks0n]

I met with same issue just now. After removing stop codon ( which is * in the input ) before sequence alignment, everything just went well.
BTW, I used the following command to remove " * " in the sequence file.
cat input.fa | sed 's/*$//g' | sed 's/\.$//g' > input.clean.fa

[YiyanYang0728]

I also encountered this problem... I changed the file extension, tried other fasta files, changed sequence names. None of them worked. I am asking for help. Thank you.

[akarimizade]

I am new to using Trimal and I had the same issue. By removing the stop codons, I successfully ran the program.

[eselimnl]

In my case, getting rid of * and # characters in the alignment solved the issue.