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)