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

AUTHOR

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