prettyplot - Draw a sequence alignment with pretty formatting

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           Wrote the script used to autogenerate this manual page.

       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).

       This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package. It can be
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EMBOSS 6.4.0                                       05/11/2012                                     PRETTYPLOT(1e)

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).

       prettyplot - Draw a sequence alignment with pretty formatting

Inputsection-sequencesseqset-matrixfilematrix
           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.

   Additionalsection-residuesperlineinteger
           The number of residues to be displayed on each line Default value: 50

       -resbreakinteger
           Default value: $(residuesperline)

       -ccoloursboolean
           Default value: Y

       -cidentitystring
           Default value: RED

       -csimilaritystring
           Default value: GREEN

       -cotherstring
           Default value: BLACK

       -docolourboolean
           Default value: N

       -shadestring
           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.

       -pairarray
           Default value: 1.5,1.0,0.5

       -identityinteger-boxboolean
           Default value: Y

       -boxcolboolean
           Default value: N

       -boxusestring
           Default value: GREY

       -nameboolean
           Default value: Y

       -maxnameleninteger
           Default value: 10

       -numberboolean
           Default value: Y

       -listoptionsboolean
           Default value: Y

       -pluralityfloat
           Default value: @( $(sequences.totweight) / 2)

   Consensussection-consensusboolean
           Default value: N

       -collisionboolean
           Default value: Y

       -alternativelist
           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.

       -showscoreinteger
           Default value: -1

       -portraitboolean
           Default value: N

   Outputsection-graphgraph

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

prettyplot-sequencesseqset [-matrixfilematrix] [-residuesperlineinteger] [-resbreakinteger]
                  [-ccoloursboolean] [-cidentitystring] [-csimilaritystring] [-cotherstring]
                  [-docolourboolean] [-shadestring] [-pairarray] [-identityinteger] [-boxboolean]
                  [-boxcolboolean] [-boxusestring] [-nameboolean] [-maxnameleninteger] [-numberboolean]
                  [-listoptionsboolean] [-pluralityfloat] [-consensusboolean] [-collisionboolean]
                  [-alternativelist] [-showscoreinteger] [-portraitboolean] -graphgraphprettyplot-help