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NEXPLOT(1)	      User Contributed Perl Documentation	    NEXPLOT(1)

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

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

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 Characters 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

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

FILES
       $Id: nexplot.pl,v 1.36 2006/08/24 06:41:57 thladish Exp $

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

SEE ALSO
       perl(1)

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

perl v5.24.1			  2006-08-24			    NEXPLOT(1)

NAME | SYNOPSIS | OPTIONS | DESCRIPTION | FILES | REQUIRES | SEE ALSO | AUTHOR

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