NAME

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

SYNOPSIS

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

OPTIONS

       -indextype
           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)

       -indexname
           Basename of encseq to construct. (default: undefined)

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

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

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

       -dc
           specify difference cover value (default: 0)

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

       -v
           be verbose (default: no)

       -help
           display help for basic options and exit

       -help+
           display help for all options and exit

       -version
           display version information and exit

DESCRIPTION

       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.

AUTHOR

       Report bugs to <willrodt@zbh.uni-hamburg.de>.

                                                   10/07/2012                                   GT-GENOMEDIFF(1)