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.
Take a look at LASTZ. You may want to look at the link that says (newer versions, unreleased).
Note that at least one option to get the sequence outputted is to use the delta2maf program. The program is not part of mummer but I uploaded it here https://github.com/cmdcolin/whole_genome_alignment_pipeline/tree/master/util