Arlin Stoltzfus > Bio-NEXUS > nexplot.pl

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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)
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