'\" t
.\"     Title: augustus
.\"    Author: [see the "AUTHOR(S)" section]
.\" Generator: Asciidoctor 2.0.20
.\"      Date: 
.\"    Manual: \ \&
.\"    Source: \ \&
.\"  Language: English
.\"
.TH "AUGUSTUS" "1" "" "\ \&" "\ \&"
.ie \n(.g .ds Aq \(aq
.el       .ds Aq '
.ss \n[.ss] 0
.nh
.ad l
.de URL
\fI\\$2\fP <\\$1>\\$3
..
.als MTO URL
.if \n[.g] \{\
.  mso www.tmac
.  am URL
.    ad l
.  .
.  am MTO
.    ad l
.  .
.  LINKSTYLE blue R < >
.\}
.SH "NAME"
augustus \- a gene prediction tool
.SH "SYNOPSIS"
.sp
\fBaugustus\fP [parameters] \-\-species=SPECIES queryfilename
.SH "OPTIONS"
.sp
The mandatory option \*(Aqqueryfilename\*(Aq specifies the filename (including relative path) to the file containing the query sequence(s) in FASTA format.
.sp
SPECIES is an identifier for the species. Use \fB\-\-species=help\fP to see a list.
.SS "Further parameters:"
.sp
\fB\-\-strand=both\fP, \fB\-\-strand=forward\fP or \fB\-\-strand=backward\fP
.RS 4
define the strand to search on
.RE
.sp
\fB\-\-genemodel=genemodel\fP
.RS 4
where genemodel is one of:
.sp
.RS 4
.ie n \{\
\h'-04'\(bu\h'+03'\c
.\}
.el \{\
.  sp -1
.  IP \(bu 2.3
.\}
partial      \- allow prediction of incomplete genes at the sequence boundaries (default)
.RE
.sp
.RS 4
.ie n \{\
\h'-04'\(bu\h'+03'\c
.\}
.el \{\
.  sp -1
.  IP \(bu 2.3
.\}
intronless   \- only predict single\-exon genes like in prokaryotes and some eukaryotes
.RE
.sp
.RS 4
.ie n \{\
\h'-04'\(bu\h'+03'\c
.\}
.el \{\
.  sp -1
.  IP \(bu 2.3
.\}
complete     \- only predict complete genes
.RE
.sp
.RS 4
.ie n \{\
\h'-04'\(bu\h'+03'\c
.\}
.el \{\
.  sp -1
.  IP \(bu 2.3
.\}
atleastone   \- predict at least one complete gene
.RE
.sp
.RS 4
.ie n \{\
\h'-04'\(bu\h'+03'\c
.\}
.el \{\
.  sp -1
.  IP \(bu 2.3
.\}
exactlyone   \- predict exactly one complete gene
.RE
.RE
.sp
\fB\-\-singlestrand=true\fP
.RS 4
predict genes independently on each strand, allow overlapping genes on opposite strands.
This option is turned off by default.
.RE
.sp
\fB\-\-hintsfile=hintsfilename\fP
.RS 4
When this option is used the prediction considering hints (extrinsic information) is turned on.
hintsfilename contains the hints in gff format.
.RE
.sp
\fB\-\-AUGUSTUS_CONFIG_PATH=path\fP
.RS 4
path to config directory (if not specified as environment variable)
.RE
.sp
\fB\-\-alternatives\-from\-evidence=true/false\fP
.RS 4
report alternative transcripts when they are suggested by hints
.RE
.sp
\fB\-\-alternatives\-from\-sampling=true/false\fP
.RS 4
report alternative transcripts generated through probabilistic sampling
.RE
.sp
\fB\-\-maxtracks=n\fP
.RS 4
For a description of these parameters see section "SAMPLING: ALTERNATIVE TRANSCRIPTS AND POSTERIOR PROBABILITIES" of docs/RUNNING\-AUGUSTUS.md.
.RE
.sp
\fB\-\-proteinprofile=filename\fP
.RS 4
When this option is used the prediction will consider the protein profile provided as parameter.
The protein profile extension is described in section "AUGUSTUS\-PPX" of docs/RUNNING\-AUGUSTUS.md.
.RE
.sp
\fB\-\-progress=true\fP
.RS 4
show a progressmeter
.RE
.sp
\fB\-\-gff3=on/off\fP
.RS 4
output in gff3 format
.RE
.sp
\fB\-\-predictionStart=A\fP, \fB\-\-predictionEnd=B\fP
.RS 4
A and B define the range of the sequence for which predictions should be found.
.RE
.sp
\fB\-\-UTR=on/off\fP
.RS 4
predict the untranslated regions in addition to the coding sequence. This currently works only for a subset of species.
.RE
.sp
\fB\-\-noInFrameStop=true/false\fP
.RS 4
Do not report transcripts with in\-frame stop codons. Otherwise, intron\-spanning stop codons could occur. Default: false
.RE
.sp
\fB\-\-noprediction=true/false\fP
.RS 4
If true and input is in genbank format, no prediction is made. Useful for getting the annotated protein sequences.
.RE
.sp
\fB\-\-uniqueGeneId=true/false\fP
.RS 4
If true, output gene identifyers like this: seqname.gN
.RE
.sp
\fB\-\-paramlist\fP
.RS 4
Show full list of supported parameters.
.RE
.SH "AUTHORS"
.sp
AUGUSTUS was written by M. Stanke, O. Keller, S. König, L. Gerischer and L. Romoth.
.SH "ADDITIONAL DOCUMENTATION"
.sp
An exhaustive documentation can be found in the file /usr/share/doc/augustus/README.md.gz.