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
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).
-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.
-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 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
-graph graph
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).
prettyplot is fully documented via the tfm(1) system.
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.