I have a number of nucleotide sequences and I would like to check
them for homology to each other.
I'd like to build a square matrix with the sequence names as rows and
columns, and (as value) a measure of homology from the bl2seq output.
One way to do this could be:
1) download Blast
2) use BlastStandAlone iteratively to get all the possible combinations
3) parse with BPbl2seq
4) build the matrix with the parameter I want
I just wanted to check if this is the way to go...