estwise - options: dna/protein

-u

start position in dna

-v

end position in dna

-trev

reverse complement dna

-tfor

use forward strands only

-both

[default] do both strands

-tabs

Positions reported as absolute to DNA

-s

start position in protein

-t

end position in protein

-gap

[ 12] gap penalty

-ext

[ 2] extension penalty

-matrix

[blosum62.bla] Comparison matrix

-hmmer

Protein file is HMMer 1.x file

-hname

Name of HMM rather than using the filename