Still new to all this, but I am looking at a collection of similar sequences that are of the same length. I had been using Mummer to align the sequences to a reference. Unfortunately I have been doing it in a cumbersome way by extracting the aligned sequence with Bioperl based on the coord file from Mummer. I did not realize that by doing it this way I am not accounting for large deletions and possibly insertions (meaning my extracted sequences has no gaps when there should be).

My understanding is I should be looking for global alignment but with these indels would I want glocal alignment? What would be best for this if Mummer cannot do this? I feel mummer's algorithm would be perfect for glocal alignment but I don't know how to make it just give me a fasta file as oppose to delta/coord files.

Also I have been testing MAFFT and Tcoffee for this and they work well as far as I can tell. I am just wondering if that is overkill since they are Multiple sequence aligners.