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]