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GT-GENOMEDIFF(1) | GenomeTools Manual | GT-GENOMEDIFF(1) |
NAME¶
gt-genomediff - Calculates Kr: pairwise distances between genomes.SYNOPSIS¶
gt genomediff [option ...] (INDEX | -indexname NAME SEQFILE SEQFILE [...])DESCRIPTION¶
-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 [string]
Basename of encseq to construct. (default:
undefined)
-unitfile [filename]
specifies genomic units, see below for description.
(default: undefined)
-mirrored [yes|no]
virtually append the reverse complement of each sequence
(default: no)
-pl [value]
specify prefix length for bucket sort recommendation: use
without argument; then a reasonable prefix length is automatically determined.
(default: 0)
-dc [value]
specify difference cover value (default: 0)
-memlimit [string]
specify maximal amount of memory to be used during index
construction (in bytes, the keywords MB and GB are allowed)
(default: undefined)
-scan [yes|no]
do not load esa index but scan it sequentially. (default:
yes)
-thr [value]
Threshold for difference (du, dl) in divergence
calculation. default: 1e-9
-abs_err [value]
absolute error for expected shulen calculation. default:
1e-5
-rel_err [value]
relative error for expected shulen calculation. default:
1e-3
-M [value]
threshold for minimum logarithm. default: DBL_MIN
-v [yes|no]
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
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 (in Lua syntax):
units = { genome1 = { "path/file1.fa", "file2.fa" }, genome2 = { "file3.fa", "path/file4.fa" } }
$ gt encseq info INDEXNAME
REPORTING BUGS¶
Report bugs to <willrodt@zbh.uni-hamburg.de>.07/29/2016 | GenomeTools 1.5.9 |