alignment sequence reading with stop codons (bug?)

[Luke McCarthy]

David Bauer wrote:
> 
> I also guess you are misinterpreting the -seqall. This means to return
> all sequences from a file containing more than one sequence (like a
> fasta formated file with several sequences separated by theire
> description lines). For me the -seqall option does not make much sense
> in the case of alignment programs which need exactly 2 sequences to
> align.

Nevertheless, the acd files for water and needle clearly state that the
second argument is a parameter of type seqall.  Which makes perfect
sense if one wants to align a probe sequence against a database of
others (a la BLAST)

Cheers,

Luke