[BiO BB] Calculate pairwise DNA percent identity in a set of data

[Jeremy Yan]

Hello,

I need a software that can calculate pairwise DNA percent identity. I know
MegAlign from DNAStar can do it, but it can only give you one decimal which
is not enough for me.

I have ever used a command line program to do it and get up to 5 decimal,
such as "0.95488". But after a day of searching, I could not find out which
program I used.

The kind of percent identity is just something for very similar sequences. I
have 18 sequences, no gap, they have percent identity from approximately
95%-99.x%. I need a more accurate percentage to calculate any pair of
sequence, how many mismatch there are, i.e. the number of nucleotide
differences. So if there is any software can just count how the number of
nucleotide differences between  any pair of sequences in a set of data, that
works as well.

Thank you very much for the help!

Jeremy