short sequence alignment to short sequence

Question

[xzpgocxx]

Hi,

I have many short sequences (60bp) and want to alignment to the short reference sequence (also is 60bp) to get the different alignment types. I have to try blast to do this work and output m8 format to get the mismatches and gap value. But It's not enough and I'm interested abundant information.

So, what software can instead the blast to do the alignment?

Thanks.

Answer 1

[mkk2152]

I use vsearch for a similar purpose, but I too would like to find other tools that would be good for this.