NAME

snap-hmm - Semi-HMM-based Nucleic Acid Parser

SYNOPSIS

snap-hmm [options] <HMM file> <FASTA file> [options]

OPTIONS

-help

report useful information

-lcmask

treat lowercase as N

-plus

predict on plus strand only

-minus

predict on minus strand only

-gff

output annotation as GFF

-ace

output annotation as ACED

-quiet

do not send progress to STDERR

-aa <file>

create FASTA file of proteins

-tx <file>

create FASTA file of transcripts

-xdef <file>

external definitions

-name <string>

name for the gene [default snap]