---
name: "chain2dim"
section: "1"
platform: "linux"
package: "vmatch"
version: "2.3.1+dfsg-9"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/chain2dim"
---

# chain2dim(1)

two-dimensional match chaining

## NAME

chain2dim - two-dimensional match chaining

## SYNOPSIS

**chain2dim** \[options\] \<matchfile\>

## OPTIONS

- **-global** \<param\>

  Global chaining. Optional parameter "gc" switches on gap costs (according to L1-model). Optional parameter "ov" means that overlaps between matches are allowed.

- **-local** \<param\>

  Compute local chains (according to L1-model). If no parameter is given, compute local chains with maximum 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** \<factor\>

  Specify weight factor \> 0.0 to obtain the score of a fragment. Requires one of the options **-local**, **-global gc** or **-global ov**.

- **-maxgap** \<width\>

  Maximal width of gap in chain.

- **-outprefix** \<prefix\>

  Specify prefix of files to output chains.

- **-withinborders**

  Only compute chains which do not cross sequence borders (not possible for matches in open format).

- **-thread** \<keywords...\>

  Thread the chains, i.e. close the gaps. Accepts an optional list of keywords "minlen1 minlen2 maxerror1 maxerror2", each followed by a number specifies the minimum length and the maximum error rate of thread. 1 refers to match instance in indexed sequence, 2 refers to matching instance in query.

- **-silent**

  Do not output the chains and only report their lengths and scores.

- **-v**

  Be verbose.

- **-version**

  Show the version of the Vmatch package.

- **-help**

  Show help.

## SEE ALSO

[vmatch(1)](/vmatch/1.md)