---
name: "gt-chain2dim"
section: "1"
platform: "linux"
package: "genometools"
version: "1.6.5+ds-2.2"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/gt-chain2dim"
---

# gt-chain2dim(1)

Chain pairwise matches.

## 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\>.