get_data
Title : get_data
Usage : NA
Function: NA
Returns : NA
Args : NAset_data
Title : set_data
Usage : NA
Function: NA
Returns : NA
Args : NArgb2hex
Title : rgb2hex
Usage : NA
Function: NA
Returns : NA
Args : NAcheckNumber
Title : checkNumber
Usage : NA
Function: NA
Returns : NA
Args : NAisNumber
Title : isNumber
Usage : NA
Function: NA
Returns : NA
Args : NAparse_number
Title : parse_number
Usage : NA
Function: NA
Returns : NA
Args : NAAssignStateToNode
Title : AssignStateToNode
Usage : NA
Function: NA
Returns : NA
Args : NAAssignStateToSuperNode
Title : AssignStateToSuperNode
Usage : NA
Function: NA
Returns : NA
Args : NAAssignStateToSubNode
Title : AssignStateToSubNode
Usage : NA
Function: NA
Returns : NA
Args : NAswap_children
Title : swap_children
Usage : NA
Function: NA
Returns : NA
Args : NAnew
Title : new
Usage : NA
Function: NA
Returns : NA
Args : NANAME
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.pmSEE ALSO
perl(1)AUTHOR
Vivek Gopalan, Micheal Cheng, Weigang Qiu (with Peter Yang, Brendan O'Brien, and Arlin Stoltzfus)