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PRETTYPLOT(1e) EMBOSS Manual for Debian PRETTYPLOT(1e)

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.
05/11/2012 EMBOSS 6.4.0