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Bio::NEXUS::Tools::NexUsertContributed Perl DoBio::NEXUS::Tools::NexPlotter(3) 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 $ 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) perl v5.32.1 2008-06-16 Bio::NEXUS::Tools::NexPlotter(3)
NAME | REQUIRES | SEE ALSO | AUTHOR
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