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Bio::Graphics::Glyph::UseroContributed PerBio::Graphics::Glyph::phylo_align(3)

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.

perl v5.24.1			  2017-07-Bio::Graphics::Glyph::phylo_align(3)

NAME | SYNOPSIS | DESCRIPTION | BUGS | SEE ALSO | AUTHORS

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