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Bio::NEXUS::Tools::NexUsertContributed Perl DoBio::NEXUS::Tools::NexPlotter(3)

   get_data
	Title	: get_data
	Usage	: NA
	Function: NA
	Returns	: NA
	Args	: NA

   set_data
	Title	: set_data
	Usage	: NA
	Function: NA
	Returns	: NA
	Args	: NA

   rgb2hex
	Title	: rgb2hex
	Usage	: NA
	Function: NA
	Returns	: NA
	Args	: NA

   checkNumber
	Title	: checkNumber
	Usage	: NA
	Function: NA
	Returns	: NA
	Args	: NA

   isNumber
	Title	: isNumber
	Usage	: NA
	Function: NA
	Returns	: NA
	Args	: NA

   parse_number
	Title	: parse_number
	Usage	: NA
	Function: NA
	Returns	: NA
	Args	: NA

   AssignStateToNode
	Title	: AssignStateToNode
	Usage	: NA
	Function: NA
	Returns	: NA
	Args	: NA

   AssignStateToSuperNode
	Title	: AssignStateToSuperNode
	Usage	: NA
	Function: NA
	Returns	: NA
	Args	: NA

   AssignStateToSubNode
	Title	: AssignStateToSubNode
	Usage	: NA
	Function: NA
	Returns	: NA
	Args	: NA

   swap_children
	Title	: swap_children
	Usage	: NA
	Function: NA
	Returns	: NA
	Args	: NA

   new
	Title	: new
	Usage	: NA
	Function: NA
	Returns	: NA
	Args	: NA

NAME
       nexplot.pl - PostScript plot of tree + data table (from NEXUS infile)

	       =head1 SYNOPSIS

	       nexplot.pl [options] foo.nex [tree_name]	> foo.ps

	       =head1 OPTIONS

	       -h	       Brief help message
	       -d	       Full documentation
	       -v	       Verbose mode
	       -V	       Print version information and quit

       -f	 Specify output	file (default: STDOUT)

	       INFORMATION TO DISPLAY
	       -b	       Turn on bootstrap values, if any
	       -i	       Turn on internal	node labeling
       -t	       Tree only (ignore any characters)
	       -I	       Specify character block (by "Title") to be used in matrix
	       (e.g. "dna", "protein", "intron")
       -m	       Matrix only (ignore any trees)
	       -c	       Cladogram mode:
       (auto if	no branch lengths present in tree)
	       normal: all branch lengths equal
	       accelerated: same as normal except OTUs are aligned at end
	       -U	       Display taxa sets in color (-U "set1 color1 [set2 color2	...]")
	       Color options are red, orange, green, forest, aqua, blue,
	       purple, pink, brown, gray, black

	       PLOT FORMATTING
	       -r	       Right-justify labels (default: left-justified)
       -C	       Columns of characters per block (default	= 10)
	       -T	       Specify tree width (longest branch; default: 10")
	       -S	       Spacing (vertically) between OTUs (default: .25")
	       -R	       Ratio of	font height to Spacing (default: 0.8; rec: 0.5-1)
	       -F	       Font to use for labels and titles
	       -B	       Draw a box indicating postscript\'s bounds of the plot area
	       -g	       Include gray lines after	OTU labels,
	       even if -t (tree	only) option is	used

	       PAGE SETUP
	       -s	       Print on	multiple pages,	but shrink to page height
	       -o	       Print on	multiple pages at actual size
	       -W	       Specify output page width (default: 8.5")
	       -H	       Specify output page height (default: 11")
	       -a	       Change page dimensions to fit plot

	       =head1 DESCRIPTION

	       B<This program> will read a NEXUS file and output a PostScript display of trees (one file for each tree
			       in the tree block), as well as any character matrix (e.g. sequences) if present in the file.

	       =head1 FILES

	       =over 4

	       =back
	       =head1 VERSION

	       $Id: NexPlotter.pm,v 1.2	2008/06/16 19:53:41 astoltzfus Exp $

REQUIRES
	       Perl 5.004, Getopt::Std,	Pod::Usage, NEXUS.pm

SEE ALSO
	     perl(1)

AUTHOR
	     Vivek Gopalan, Micheal Cheng, Weigang Qiu (with Peter Yang, Brendan O'Brien, and Arlin Stoltzfus)

perl v5.24.1			  2008-06-16  Bio::NEXUS::Tools::NexPlotter(3)

NAME | REQUIRES | SEE ALSO | AUTHOR

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