NAME

pppplot.pl - generates posterior probability of presence plots (SPAN)

SYNOPSIS

pppplot.pl <filelist>

where <filelist> is a file with the names (one name per line) of data files generated by prob-changes.pl. The PostScript output file will be named "filelist.ps" if the plots all fit on one page, or "filelist-<n>.ps" if they are distributed on multiple pages.

DESCRIPTION

pppplot.pl generates a phylogenetic probability of presence (ppp) plot. In the context of SPAN this typically is used to display the history or one or more intron characters on a phylogenetic tree. If the input file lists multiple data files, pppplot.pl determines how many pages of output to produce, and how many figures to put on each page.

pppplot.pl generates its clever graphics by opening a named pipe to execute commands in the R data analysis language. This does not work on all systems. In particular, the current implementation of Perl on Mac OS X does not support named pipes.

The PPP plot is an idea by Weigang Qiu.

VERSION

$Id: pppplot.pl,v 1.4 2003/09/25 20:23:28 arlin Exp $

REQUIRES

R, via named pipe (see DESCRIPTION)

AUTHOR

Arlin Stoltzfus (stoltzfu@umbi.umd.edu)

To install Bio::NEXUS, copy and paste the appropriate command in to your terminal.

cpanm

cpanm Bio::NEXUS

CPAN shell

perl -MCPAN -e shell
install Bio::NEXUS

For more information on module installation, please visit the detailed CPAN module installation guide.

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