FASTA program discussion list

[William Pearson <>]

James --

Unfortunately, this difference reflects some historical differences in the 
lalign output structure compared with the fasta searching programs.  
Basically, the function that produces the text that begins "The best scores 
are:" is used to produce --m 8 and -m 9 output, and that function is not used 
by lalign.

I agree that it is inconvenient, and plan to address the problem in an 
upcoming release.

Sorry,

Bill Pearson