Some questions in execution in command line mode in CLUSTALW

ABC cdcer at hongkong.com
Mon Jun 30 07:20:24 EST 2003

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, ...


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