align.seqs of different length

I have some sequences in a few fasta files processed before and I want to put it together and make dist.seqs + cluster to them.

I ran merge.files before doing dist.seqs, and then I got the message that my sequences are not of the same length, so I tried to do align.seqs, but I found the same problem.

How can I do it? Is it possible to run align.seqs with sequences of different length?

Thank you very much

You shouldn’t have a problem running align.seqs and then using the align file it generates. I’d suggest following along with the SOP because there are a few steps between aligning and calculating distances.