Provided by: augustus_3.3.1+dfsg-1_amd64 bug


       homGeneMapping - create summary of gene homology


       homGeneMapping [options] --gtfs=gffilenames.tbl --halfile=aln.hal


       homGeneMapping takes a set of gene predictions of different genomes and a hal alignment of
       the genomes and prints a summary for each gene, e.g.

       ·   how many of its exons/introns are in agreement with genes of other genomes

       ·   how many of its exons/introns are supported by extrinsic evidence from any of the

       ·   a list of geneids of homologous genes


   Mandatory parameters
           input hal file

           a text file containing the locations of the input gene files and optionally the hints
           files (both in GTF format). The file is formatted as follows:

               name_of_genome_1  path/to/genefile/of/genome_1  path/to/hintsfile/of/genome_1
               name_of_genome_2  path/to/genefile/of/genome_2  path/to/hintsfile/of/genome_2
               name_of_genome_N  path/to/genefile/of/genome_N  path/to/hintsfile/of/genome_N

   Additional options
           N is the number of CPUs to use (default: 1)

           do not map between duplications in hal graph. (default: off)

           Directory that contains the executable halLiftover If not specified it must be in
           $PATH environment variable.

           a temporary file directory that stores lifted over files. (default 'tmp/' in current

           file direcory that stores output gene files. (default: current directory)

           prints disjunct sets of homologous transcripts to FILE, e.g.

               # 0     dana
               # 1     dere
               # 2     dgri
               # 3     dmel
               # 4     dmoj
               # 5     dper
               (0, jg4139.t1) (0, jg4140.t1) (1, jg7797.t1) (2, jg3247.t1) (4, jg6720.t1) (5, jg313.t1)
               (1, jg14269.t1) (3, jg89.t1) (5, jg290.t1)
               Two transcripts are in the same set, if all their exons/introns are homologs and their are
               no additional exons/introns.
               This option requires the Boost C++ Library


       homGeneMapping --noDupes
       --gtfs=gtffilenames.tbl --halfile=msca.hal


       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/augustus/README.TXT.