psw - options

-g

gap penalty (default 12) - gap penalty used for smith waterman

-e

ext penatly (default 2) - ext penalty used for smith waterman

-m

comp matrix (default blosum62.bla) - comparison matrix used for both smith waterman and the abc model

-abc

use the abc model: use Stephen Altschul's 'generalised gap penalty' model (called the abc model in Wise2)

-a

a penalty for above (default 120) gap opening penalty in the abc model

-b

b penalty for above (default 10) gap extension penalty in the abc model

-c

c penalty for above (default 3) unmatched 'gap' region penalty in the abc model

-max_desc

Maximum number of description lines

-max_aln

Maximum number of alignments

-ids

in alignments, show sequence names, not probe/target

-r

show raw output - raw matrix output

-l

show label output - label based output

-f

show fancy output - pretty output