Mutations statistics software?

Question

[lokapal]

Hello, people!

I need in the simplest (as it seems to me) program that can analyze multiple alignment file containing one reference DNA sequence and not-so-many other sequences (less than 20) and report all mutations statistics: number of mutations, their type etc. This is not NGS task, it's "classic" multiple alignment and length of alignment varies from 240 to 550 bp. I cannot find anything that can be used for this task. Any advice would be appreciated, thanks in advance!

[arnstrm]

If you don't have a lot of data, how about you just do a multiple alignment, manually trim the alignment ends, and mask all the common nucleotides (just changing the view using programs such as bioedit/mega). You can easily spot the changes/substitutions in the sequences. This is assuming you have highly identical sequences, if not it will be tedious.