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

- NAME
- SYNOPSIS
- DESCRIPTION

- OPTIONS

- BUGS
- SEE ALSO
- AUTHORS

# NAME

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

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# SYNOPSIS

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

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# 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 the Bio::Graphics::Glyph manpage 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

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# BUGS

Please report them.

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# SEE ALSO

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

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# 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.

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