.TH HMM-ASSEMBLER.PL "1" "November 2013" "hmm-assembler.pl 2010-07-28" "User Commands"
.SH NAME
hmm-assembler.pl \- SNAP module hmm-assembler.pl
.SH SYNOPSIS
.B hmm-assembler.pl
[\fI-OPTIONS \fR[\fI-MORE_OPTIONS\fR]] [\fI--\fR] [\fIPROGRAM_ARG1 \fR...]
.SH OPTIONS
.SS "The following single-character options are accepted:"
.PP
With arguments: \fB\-i\fR \fB\-e\fR \fB\-A\fR \fB\-D\fR \fB\-M\fR \fB\-S\fR \fB\-C\fR \fB\-I\fR \fB\-N\fR \fB\-a\fR \fB\-3\fR \fB\-5\fR \fB\-Z\fR \fB\-c\fR
.PP
Boolean (without arguments): \fB\-r\fR \fB\-o\fR \fB\-x\fR \fB\-p\fR \fB\-t\fR \fB\-1\fR
.PP
Options may be merged together.  \fB\-\-\fR stops processing of options.
Space is not required between options and their arguments.
.PP
Options:
.TP
\fB\-i\fR
<length>       [500]
.TP
\fB\-e\fR
<length>       [1000]
.TP
\fB\-A\fR
<order:length> [0:30]
.TP
\fB\-D\fR
<order:length> [0:9]
.TP
\fB\-M\fR
<order:length> [0:15]
.TP
\fB\-S\fR
<order:length> [0:9]
.TP
\fB\-C\fR
<order>        [4]
.TP
\fB\-I\fR
<order>        [4]
.TP
\fB\-N\fR
<order>        [4]
.TP
\fB\-3\fR
<order:length> []  include 3'UTR model, requires \fB\-a\fR
.TP
\fB\-a\fR
<order:length> []  include PolyA model, requires \fB\-3\fR
.TP
\fB\-5\fR
<order:length> []  include 5'UTR moel, requires \fB\-p\fR
.TP
\fB\-p\fR
include generic promoter model, requires \fB\-5\fR
.TP
\fB\-r\fR
include generic repeat model
.TP
\fB\-o\fR
include reverse ORF model
.TP
\fB\-x\fR
use explicit duration intron model
.TP
\fB\-t\fR
include C.elegans trans\-splicing, requires \fB\-p\fR, \fB\-5\fR
.TP
\fB\-Z\fR
<clade>            sets clade\-specific values (worm, fly, plant)
.TP
\fB\-1\fR
single gene model
.TP
\fB\-c\fR <score>
include GC\-AG splice donor model