Suppose I have 2 groups of sequences. A has 10 and B has 5.
I could make a.fa and b.fa to do the alignment respectively.
1. What I want is to do the alignment of each sequence in B to A.
In other words, I want to find out the score of each bi to each ai.
How do I do in CLUSTALW (in LINUX command line mode based).
2. How could I do this by other program, like Perl script?
3. Could I conver the output in other formats? I fail to do so by just
seting -ouput=fasta, ...