Provided by: augustus_3.4.0+dfsg2-3build1_amd64 bug


       augustus - a gene prediction tool


       augustus [parameters] --species=SPECIES queryfilename


       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.

   Further parameters:
       --strand=both, --strand=forward or --strand=backward
           define the strand to search on

           where genemodel is one of:

           ·   partial      - allow prediction of incomplete genes at the sequence boundaries

           ·   intronless   - only predict single-exon genes like in prokaryotes and some

           ·   complete     - only predict complete genes

           ·   atleastone   - predict at least one complete gene

           ·   exactlyone   - predict exactly one complete gene

           predict genes independently on each strand, allow overlapping genes on opposite
           strands. This option is turned off by default.

           When this option is used the prediction considering hints (extrinsic information) is
           turned on. hintsfilename contains the hints in gff format.

           path to config directory (if not specified as environment variable)

           report alternative transcripts when they are suggested by hints

           report alternative transcripts generated through probabilistic sampling

           For a description of these parameters see section 4 of README.TXT.

           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.

           show a progressmeter

           output in gff3 format

       --predictionStart=A, --predictionEnd=B
           A and B define the range of the sequence for which predictions should be found.

           predict the untranslated regions in addition to the coding sequence. This currently
           works only for a subset of species.

           Do not report transcripts with in-frame stop codons. Otherwise, intron-spanning stop
           codons could occur. Default: false

           If true and input is in genbank format, no prediction is made. Useful for getting the
           annotated protein sequences.

           If true, output gene identifyers like this: seqname.gN

           Show full list of supported parameters.


       AUGUSTUS was written by M. Stanke, O. Keller, S. König, L. Gerischer and L. Romoth.


       An exhaustive documentation can be found in the file /usr/share/doc/augustus/