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.IX Title "Bio::Graphics::Glyph::phylo_align 3pm"
.TH Bio::Graphics::Glyph::phylo_align 3pm "2018-09-21" "perl v5.26.2" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
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.SH "NAME"
Bio::Graphics::Glyph::phylo_align \- The "phylogenetic alignment" glyph
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 1
\&  See L<Bio::Graphics::Panel> and L<Bio::Graphics::Glyph>.
.Ve
.SH "DESCRIPTION"
.IX Header "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 \s-1CIGAR\s0 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.
.PP
For this glyph to work, the feature must return a \s-1DNA\s0 sequence string
in response to the \fIdna()\fR method.  Also, a valid tree file must be
available in a format readable by the Bio::Tree library.
.SS "\s-1OPTIONS\s0"
.IX Subsection "OPTIONS"
The following options are standard among all Glyphs.  See
Bio::Graphics::Glyph for a full explanation.
.PP
.Vb 2
\&  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)
.Ve
.PP
In addition to the common options, the following glyph-specific
options are recognized:
.PP
.Vb 2
\&  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
.Ve
.SH "BUGS"
.IX Header "BUGS"
Please report them.
.SH "SEE ALSO"
.IX Header "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,
\&\s-1GD\s0
.SH "AUTHORS"
.IX Header "AUTHORS"
Hisanaga Mark Okada
Lincoln Stein <lstein@cshl.org>.
.PP
Copyright (c) 2001 Cold Spring Harbor Laboratory
.PP
This library is free software; you can redistribute it and/or modify
it under the same terms as Perl itself.  See \s-1DISCLAIMER\s0.txt for
disclaimers of warranty.