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PROGRAM:

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

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