I have sequencing data for 3 species from 4 sites.The sequences are from
the Cytochrome Oxidase I gene.I have 10-18 sequences per site per species.
I aligned them using ABI-PE software for 373 synthesizer to arrive at
Now my goal is to compare the same species in different sites to see if
differences exist in the consensus sequences between sites.
Can someone suggst a program that I can use to do this???