prettyplot1e
Draw a sequence alignment with pretty formatting
Usage
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
Overview
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
Releases
9 releases since Debian 5.0 (Lenny); the text changed 2 times.
-boxuse since Debian 6.0 (Squeeze).
-boxcolval until Debian 5.0 (Lenny).