.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.43.3.
.TH SNAP "1" "October 2013" "snap 2010-07-28" "User Commands"
.SH NAME
snap \- Semi-HMM-based Nucleic Acid Parser
.SH SYNOPSIS
.B snap
[\fIoptions\fR] <\fBHMM file\fR> <\fBFASTA file\fR> [\fIoptions\fR]
.SH OPTIONS
.TP
\fB\-help\fR
report useful information
.TP
\fB\-lcmask\fR
treat lowercase as N
.TP
\fB\-plus\fR
predict on plus strand only
.TP
\fB\-minus\fR
predict on minus strand only
.TP
\fB\-gff\fR
output annotation as GFF
.TP
\fB\-ace\fR
output annotation as ACED
.TP
\fB\-quiet\fR
do not send progress to STDERR
.TP
\fB\-aa\fR <file>
create FASTA file of proteins
.TP
\fB\-tx\fR <file>
create FASTA file of transcripts
.TP
\fB\-xdef\fR <file>
external definitions
.TP
\fB\-name\fR <string>
name for the gene [default snap]