Arlin Stoltzfus

NAME - generates posterior probability of presence plots (SPAN)

SYNOPSIS <filelist>

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

DESCRIPTION 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, determines how many pages of output to produce, and how many figures to put on each page. 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.


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


R, via named pipe (see DESCRIPTION)




Arlin Stoltzfus (