Man page or keyword search:   man All Sections 1 - General Commands 2 - System Calls 3 - Subroutines, Functions 4 - Special Files 5 - File Formats 6 - Games and Screensavers 7 - Macros and Conventions 8 - Maintenence Commands 9 - Kernel Interface New Commands Server 4.4BSD AIX Alpinelinux Archlinux Aros BSDOS BSDi Bifrost CentOS Cygwin Darwin Debian DigitalUNIX DragonFly ElementaryOS Fedora FreeBSD Gentoo GhostBSD HP-UX Haiku Hurd IRIX Inferno JazzOS Kali Knoppix LinuxMint MacOSX Mageia Mandriva Manjaro Minix MirBSD NeXTSTEP NetBSD OPENSTEP OSF1 OpenBSD OpenDarwin OpenIndiana OpenMandriva OpenServer OpenSuSE OpenVMS Oracle PC-BSD Peanut Pidora Plan9 QNX Raspbian RedHat Scientific Slackware SmartOS Solaris SuSE SunOS Syllable Tru64 UNIXv7 Ubuntu Ultrix UnixWare Xenix YellowDog aLinux   44335 pages apropos Keyword Search (all sections) Output format html ascii pdf view pdf save postscript

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 v5.20.2			  2006-08-24			    NEXPLOT(1)

Vote for polarhome