---
name: "distmat"
section: "1e"
platform: "linux"
package: "emboss"
version: "6.6.0+dfsg-15"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/distmat"
---

# distmat(1e)

Create a distance matrix from a multiple sequence alignment

## NAME

distmat - Create a distance matrix from a multiple sequence alignment

## SYNOPSIS

**distmat** **-sequence** *seqset* **-nucmethod** *list* **-protmethod** *list* **-ambiguous** *boolean* **-gapweight** *float* **-position** *integer* **-calculatea** *boolean* **-parametera** *float* **-outfile** *outfile*

**distmat** **-help**

## DESCRIPTION

**distmat** is a command line program from EMBOSS (“the European Molecular Biology Open Software Suite”). It is part of the "Phylogeny:Molecular sequence" command group(s).

## OPTIONS

### Input section

- **-sequence** *seqset*

  File containing a sequence alignment.

### Required section

- **-nucmethod** *list*

  Multiple substitution correction methods for nucleotides.

- **-protmethod** *list*

  Multiple substitution correction methods for proteins.

### Additional section

- **-ambiguous** *boolean*

  Option to use the ambiguous codes in the calculation of the Jukes-Cantor method or if the sequences are proteins. Default value: N

- **-gapweight** *float*

  Option to weight gaps in the uncorrected (nucleotide) and Jukes-Cantor distance methods. Default value: 0.

- **-position** *integer*

  Choose base positions to analyse in each codon i.e. 123 (all bases), 12 (the first two bases), 1, 2, or 3 individual bases. Default value: 123

- **-calculatea** *boolean*

  This will force the calculation of parameter 'a' in the Jin-Nei Gamma distance calculation, otherwise the default is 1.0 (see -parametera option). Default value: N

- **-parametera** *float*

  User defined parameter 'a' to be use in the Jin-Nei Gamma distance calculation. The suggested value to be used is 1.0 (Jin et al.) and this is the default. Default value: 1.0

### Output section

- **-outfile** *outfile*

  ## BUGS

Bugs can be reported to the Debian Bug Tracking system (http://bugs.debian.org/emboss), or directly to the EMBOSS developers (http://sourceforge.net/tracker/?group\_id=93650&atid=605031).

## SEE ALSO

distmat is fully documented via the **tfm**(1) system.

## AUTHOR

**Debian Med Packaging Team** \<debian-med-packaging@lists.alioth.debian.org\>

Wrote the script used to autogenerate this manual page.

## COPYRIGHT

This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package. It can be redistributed under the same terms as EMBOSS itself.