Provided by: libbio-graphics-perl_2.40-3_all bug

NAME

       Bio::Graphics::Glyph::phylo_align - The "phylogenetic alignment" glyph

SYNOPSIS

         See L<Bio::Graphics::Panel> and L<Bio::Graphics::Glyph>.

DESCRIPTION

       This glyph draws a cladogram for any set of species along with their alignment data in
       relation to the reference species.  At high magnification, base pair alignements will be
       displayed.  At lower magnification, a conservation score plot will be drawn.  Gaps as
       specified by CIGAR are supported.  Currently the scores are drawn to a log plot with the
       restriction that the score will be the same across all base pairs within an alignment.  It
       is hoped that this restriction can be addressed in the future.

       For this glyph to work, the feature must return a DNA sequence string in response to the
       dna() method.  Also, a valid tree file must be available in a format readable by the
       Bio::Tree library.

   OPTIONS
       The following options are standard among all Glyphs.  See Bio::Graphics::Glyph for a full
       explanation.

         Option      Description                      Default
         ------      -----------                      -------

         -fgcolor      Foreground color               black

         -outlinecolor Synonym for -fgcolor

         -bgcolor      Background color               turquoise

         -fillcolor    Synonym for -bgcolor

         -linewidth    Line width                     1

         -height       Height of glyph                10

         -font         Glyph font                     gdSmallFont

         -connector    Connector type                 0 (false)

         -connector_color
                       Connector color                black

         -label        Whether to draw a label        0 (false)

         -description  Whether to draw a description  0 (false)

         -hilite       Highlight color                undef (no color)

       In addition to the common options, the following glyph-specific options are recognized:

         Option      Description               Default
         ------      -----------               -------

         -draw_clado_left
                     Draws the Cladogram on left 0

         -species_spacing
                     Spacing of species in DNA   1
                     mode in units of font height

         -species_spacing_score
                     Spacing of spcies in        5
                     conservation view in units
                     of font height

         -hide_label Whether to label spcies     0

         -tree_file  Path of file containing     undef
                     cladogram tree information
         -tree_format Format of tree file         newick

         -axis_color Color of the vertical axes  fgcolor
                     in the GC content graph

         -errcolor   Color of all misalignment   fgcolor
                     indicators

         -mid_axis_color
                     Color of the middle axis of
                     the conservation score graph axis_color

         -clado_bg  Color of the clado bg       bgcolor
                     indicators

         -ref_color  Color of base pair bg for   bgcolor
                     the reference sequence

         -targ_color Color of base pair bg for   bgcolor
                     all base pairs that match
                     reference

BUGS

       Please report them.

SEE ALSO

       Bio::Graphics::Panel, Bio::Graphics::Glyph, Bio::Graphics::Glyph::arrow,
       Bio::Graphics::Glyph::cds, Bio::Graphics::Glyph::crossbox, Bio::Graphics::Glyph::diamond,
       Bio::Graphics::Glyph::dna, Bio::Graphics::Glyph::dot, Bio::Graphics::Glyph::ellipse,
       Bio::Graphics::Glyph::extending_arrow, Bio::Graphics::Glyph::generic,
       Bio::Graphics::Glyph::graded_segments, Bio::Graphics::Glyph::heterogeneous_segments,
       Bio::Graphics::Glyph::line, Bio::Graphics::Glyph::pinsertion,
       Bio::Graphics::Glyph::primers, Bio::Graphics::Glyph::rndrect,
       Bio::Graphics::Glyph::segments, Bio::Graphics::Glyph::ruler_arrow,
       Bio::Graphics::Glyph::toomany, Bio::Graphics::Glyph::transcript,
       Bio::Graphics::Glyph::transcript2, Bio::Graphics::Glyph::translation,
       Bio::Graphics::Glyph::triangle, Bio::DB::GFF, Bio::SeqI, Bio::SeqFeatureI, Bio::Das, GD

AUTHORS

       Hisanaga Mark Okada Lincoln Stein <lstein@cshl.org>.

       Copyright (c) 2001 Cold Spring Harbor Laboratory

       This library is free software; you can redistribute it and/or modify it under the same
       terms as Perl itself.  See DISCLAIMER.txt for disclaimers of warranty.