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.