prettyplot(1) Draw a sequence alignment with pretty formatting


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



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).


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 can be reported to the Debian Bug Tracking system (, or directly to the EMBOSS developers (


Debian Med Packaging Team <[email protected]>

Wrote the script used to autogenerate this manual page.


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.