Man page - gt-chain2dim(1)
Packages contas this manual
- gt-scriptfilter(1)
- gt-mmapandread(1)
- gt-gff3(1)
- gt-ltrdigest(1)
- gt-encseq(1)
- gt-extractfeat(1)
- gt-seed_extend(1)
- gt-dupfeat(1)
- gt-csa(1)
- gt-clean(1)
- gt-packedindex(1)
- gt-genomediff(1)
- gt-sketch_page(1)
- gt-compreads-refcompress(1)
- gt-splicesiteinfo(1)
- gt-extractseq(1)
- gt-compreads(1)
- gt-encseq-decode(1)
- gt-cds(1)
- gt-encseq-bitextract(1)
- gt-readjoiner(1)
- gt-tallymer-occratio(1)
- gt-tallymer(1)
- gt-sequniq(1)
- gt-id_to_md5(1)
- gt-readjoiner-prefilter(1)
- gt-seqtranslate(1)
- gt-tallymer-search(1)
- gt-condenseq(1)
- gt-seqmutate(1)
- gt-seqorder(1)
- gt-seq(1)
- gt-inlineseq_add(1)
- gt-repfind(1)
- gt-seqfilter(1)
- gt-sketch(1)
- gt-hop(1)
- gt-seqids(1)
- gt-fastq_sample(1)
- gt-compreads-refdecompress(1)
- gt-readjoiner-assembly(1)
- gt-readjoiner-overlap(1)
- gt-splitfasta(1)
- gt-seqtransform(1)
- gt-tallymer-mkindex(1)
- gt-wtree(1)
- gt-ltrharvest(1)
- gt-chseqids(1)
- gt-compreads-decompress(1)
- gt-orffinder(1)
- gt-encseq-sample(1)
- gt-encseq-md5(1)
- gt-merge(1)
- gt-gff3validator(1)
- gt-matchtool(1)
- gt-congruence(1)
- gt-tagerator(1)
- gt-gff3_to_gtf(1)
- gt-featureindex(1)
- gt-md5_to_id(1)
- gt-mkfeatureindex(1)
- gt-tirvish(1)
- gt-snpper(1)
- gt-prebwt(1)
- gt-stat(1)
- gt-speck(1)
- gt-convertseq(1)
- gt-compreads-compress(1)
- gt-interfeat(1)
- gt-chain2dim(1)
- gt-encseq-bench(1)
- gt-shulengthdist(1)
- gt-encseq-encode(1)
- gt-select(1)
- gt-uniq(1)
- gt-shredder(1)
- gt-fingerprint(1)
- gt-matstat(1)
- gt-encseq-info(1)
- gt-congruence-spacedseed(1)
- gt-encseq2spm(1)
- gt-simreads(1)
- gt(1)
- gt-dot(1)
- gt-ltrclustering(1)
- gt-seqstat(1)
- gt-mergefeat(1)
- gt-bed_to_gff3(1)
- gt-uniquesub(1)
- gt-gtf_to_gff3(1)
- gt-eval(1)
- gt-encseq-check(1)
- gt-loccheck(1)
- gt-inlineseq_split(1)
Package: genometools
apt-get install genometools
apt-get install genometools
Manuals in package:
Documentations in package:
Manual
| GT-CHAIN2DIM(1) | GenomeTools Manual | GT-CHAIN2DIM(1) |
NAME
gt-chain2dim - Chain pairwise matches.
SYNOPSIS
gt chain2dim [options] -m matchfile
DESCRIPTION
-m [filename]
Specify file containing the matches mandatory option
(default: undefined)
-global
perform global chaining
•optional parameter gc switches on gap costs
(according to L1-model)
•optional parameter ov means that overlaps between
matches are allowed
•optional parameter all means that all optimal
chains are processed
-local
perform local chaining compute local chains (according to
L1-model).
•If no parameter is given, compute local chains
with maximums score.
•If parameter is given, this must be a positive
number optionally followed by the character b or p.
•If only the number, say k, is given, this is the
minimum score of the chains output.
•If a number is followed by character b, then
output all chains with the largest k scores.
•If a number is followed by character p, then
output all chains with scores at most k percent away from the best
score.
-wf [value]
specify weight factor > 0.0 to obtain score of a
fragment requires one of the options -local const -global gc -global ov
(default: 1.000000)
-maxgap [value]
specify maximal width of gap in chain (default: 0)
-silent [yes|no]
do not output the chains but only report their lengths
and scores (default: no)
-v [yes|no]
be verbose (default: no)
-help
display help and exit
-version
display version information and exit
REPORTING BUGS
Report bugs to <kurtz@zbh.uni-hamburg.de>.
| 04/27/2024 | GenomeTools 1.6.5 |