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

# prettyplot(1e)

Draw a sequence alignment with pretty formatting

## NAME

prettyplot - Draw a sequence alignment with pretty formatting

## SYNOPSIS

**prettyplot** **-sequences** *seqset* \[**-matrixfile** *matrix*\] \[**-residuesperline** *integer*\] \[**-resbreak** *integer*\] \[**-ccolours** *boolean*\] \[**-cidentity** *string*\] \[**-csimilarity** *string*\] \[**-cother** *string*\] \[**-docolour** *boolean*\] \[**-shade** *string*\] \[**-pair** *array*\] \[**-identity** *integer*\] \[**-box** *boolean*\] \[**-boxcol** *boolean*\] \[**-boxuse** *string*\] \[**-name** *boolean*\] \[**-maxnamelen** *integer*\] \[**-number** *boolean*\] \[**-listoptions** *boolean*\] \[**-plurality** *float*\] \[**-consensus** *boolean*\] \[**-collision** *boolean*\] \[**-alternative** *list*\] \[**-showscore** *integer*\] \[**-portrait** *boolean*\] **-graph** *graph*

**prettyplot** **-help**

## DESCRIPTION

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

## OPTIONS

### Input section

- **-sequences** *seqset*

  - **-matrixfile** *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.

### Additional section

- **-residuesperline** *integer*

  The number of residues to be displayed on each line Default value: 50

- **-resbreak** *integer*

  Default value: $(residuesperline)

- **-ccolours** *boolean*

  Default value: Y

- **-cidentity** *string*

  Default value: RED

- **-csimilarity** *string*

  Default value: GREEN

- **-cother** *string*

  Default value: BLACK

- **-docolour** *boolean*

  Default value: N

- **-shade** *string*

  Set to BPLW for normal shading (black, pale, light, white) so for pair = 1.5,1.0,0.5 and shade = BPLW Residues score Colour 1.5 or over... BLACK (B) 1.0 to 1.5 ... BROWN (P) 0.5 to 1.0 ... WHEAT (L) under 0.5 .... WHITE (W) The only four letters allowed are BPLW, in any order.

- **-pair** *array*

  Default value: 1.5,1.0,0.5

- **-identity** *integer*

  - **-box** *boolean*

  Default value: Y

- **-boxcol** *boolean*

  Default value: N

- **-boxuse** *string*

  Default value: GREY

- **-name** *boolean*

  Default value: Y

- **-maxnamelen** *integer*

  Default value: 10

- **-number** *boolean*

  Default value: Y

- **-listoptions** *boolean*

  Default value: Y

- **-plurality** *float*

  Default value: @( $(sequences.totweight) / 2)

### Consensus section

- **-consensus** *boolean*

  Default value: N

- **-collision** *boolean*

  Default value: Y

- **-alternative** *list*

  Values are 0:Normal collision check. (default) 1:Compares identical scores with the max score found. So if any other residue matches the identical score then a collision has occurred. 2:If another residue has a greater than or equal to matching score and these do not match then a collision has occurred. 3:Checks all those not in the current consensus.If any of these give a top score for matching or identical scores then a collision has occured.

- **-showscore** *integer*

  Default value: -1

- **-portrait** *boolean*

  Default value: N

### Output section

- **-graph** *graph*

  ## 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

prettyplot 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.