[BiO BB] Percentage sequence identity calculation program

[Lipika Ray]

Hello,

I have a set of fragments of sequences which are of different length. I
want to calculate percentage sequence identity of those sequences. Which
program will be the fittest to do this type of calculation? I have seen
that lot of databases are reporting about percentage sequence identity of
the sequences used, but by which program they calculate it, I have no idea
about that. Please help me if anyone have any clue.
Thanks in advance,

Lipika