Provided by: genometools_1.5.1-2ubuntu1_amd64 bug


       gt-genomediff - Calculates Kr: pairwise distances between genomes.


       gt genomediff [option ...] (INDEX | -indexname NAME SEQFILE SEQFILE [...])


           specify type of index, one of: esa|pck|encseq. Where encseq is an encoded sequence and
           an enhanced suffix array will be constructed only in memory. (default: encseq)

           Basename of encseq to construct. (default: undefined)

           specifies genomic units, see below for description. (default: undefined)

           virtually append the reverse complement of each sequence (default: no)

           specify prefix length for bucket sort recommendation: use without argument; then a
           reasonable prefix length is automatically determined. (default: 0)

           specify difference cover value (default: 0)

           specify maximal amount of memory to be used during index construction (in bytes, the
           keywords MB and GB are allowed) (default: undefined)

           be verbose (default: no)

           display help for basic options and exit

           display help for all options and exit

           display version information and exit


       The genomediff tool only accepts DNA input.

       When used with sequence files or encseq, an enhanced suffix array will be built in memory.
       The ESA will not be created completely, but construction will use -memlimit as a threshold
       and build it partwise, calculating the Shu-length for each part.

       File format for option -unitfile (lua):

           units = {
            genome1 = { "path/file1.fa", "file2.fa" },
            genome2 = { "file3.fa", "path/file4.fa" }

       Give the path to the files as they were given to the encseq tool! You can use gt encseq
       info INDEXNAME to get a list of files in an encoded sequence.

       Comment lines start with -- and will be ignored. See
       GTDIR/testdata/genomediff/unitfile1.lua for an example.

       Options -pl -dc -memlimit are options to influence esa construction.


       Report bugs to <>.

                                            10/07/2012                           GT-GENOMEDIFF(1)