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

# plotcon(1e)

Plot conservation of a sequence alignment

## NAME

plotcon - Plot conservation of a sequence alignment

## SYNOPSIS

**plotcon** **-sequences** *seqset* \[**-scorefile** *matrix*\] **-winsize** *integer* **-graph** *xygraph*

**plotcon** **-help**

## DESCRIPTION

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

## OPTIONS

### Input section

- **-sequences** *seqset*

  File containing a sequence alignment

- **-scorefile** *matrix*

  This is the scoring matrix file used when comparing sequences. By default it is the file 'EBLOSUM62' (for proteins) or the file 'EDNAFULL' (for nucleic sequences). These files are found in the 'data' directory of the EMBOSS installation.

### Required section

- **-winsize** *integer*

  Number of columns to average alignment quality over. The larger this value is, the smoother the plot will be. Default value: 4

### Output section

- **-graph** *xygraph*

  ## 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

plotcon 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.