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Man Pages


Manual Reference Pages  -  BIO::NEXUS::TOOLS::NEXPLOTTER (3)

.ds Aq ’

    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 $



CONTENTS

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 OBrien, and Arlin Stoltzfus)



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