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.