The mandatory option 'queryfilename' specifies the filename
(including relative path) to the file containing the query sequence(s) in
FASTA format.
SPECIES is an identifier for the species. Use
--species=help to see a list.
--strand=both, --strand=forward or
--strand=backward
define the strand to search on
--genemodel=genemodel
where genemodel is one of:
•partial - allow prediction of incomplete genes at
the sequence boundaries (default)
•intronless - only predict single-exon genes like
in prokaryotes and some eukaryotes
•complete - only predict complete genes
•atleastone - predict at least one complete
gene
•exactlyone - predict exactly one complete
gene
--singlestrand=true
predict genes independently on each strand, allow
overlapping genes on opposite strands. This option is turned off by
default.
--hintsfile=hintsfilename
When this option is used the prediction considering hints
(extrinsic information) is turned on. hintsfilename contains the hints in gff
format.
--AUGUSTUS_CONFIG_PATH=path
path to config directory (if not specified as environment
variable)
--alternatives-from-evidence=true/false
report alternative transcripts when they are suggested by
hints
--alternatives-from-sampling=true/false
report alternative transcripts generated through
probabilistic sampling
--maxtracks=n
For a description of these parameters see section 4 of
README.TXT.
--proteinprofile=filename
When this option is used the prediction will consider the
protein profile provided as parameter. The protein profile extension is
described in section 7 of README.TXT.
--progress=true
show a progressmeter
--gff3=on/off
output in gff3 format
--predictionStart=A, --predictionEnd=B
A and B define the range of the sequence for which
predictions should be found.
--UTR=on/off
predict the untranslated regions in addition to the
coding sequence. This currently works only for a subset of species.
--noInFrameStop=true/false
Do not report transcripts with in-frame stop codons.
Otherwise, intron-spanning stop codons could occur. Default: false
--noprediction=true/false
If true and input is in genbank format, no prediction is
made. Useful for getting the annotated protein sequences.
--uniqueGeneId=true/false
If true, output gene identifyers like this:
seqname.gN
--paramlist
Show full list of supported parameters.