NAME
bremer.pl - creates paup commands to calculate bremer values using parsimony ratchet.
SYNOPSIS
- perl bremer.pl
-
-f<treefile>
-l
nodelabel-p
% of chars to reweight-i
number of iterations-n
number of characters[ -h ]
DESCRIPTION
The bremer.pl program takes a newick formatted tree from a file, looks for all labels whose basename is nodelabel (e.g. if the basename is node, it'll look for node1, node2, and so on). It will then print out paup commands that run, for each found node, a parsimony ratchet search for the number of iterations specified with -i, reweighting a fraction (-p) of the -n characters. The ratchet search is performed using an inverse monophyly constraint on the tips subtended by the focal node, and so the difference between the length of shortest tree found during this ratchet search and the shortest unconstrained tree is the bremer value for the focal node.
OPTIONS AND ARGUMENTS
Note that there are no spaces between the option flags and their values.
- -f<treefile>
-
A text file containing at least one newick formatted tree description with labelled nodes.
- -l
nodelabel -
Base name of the nodes for which to write ratchet commands.
- -p
% of chars to reweight -
Number of characters to reweight during ratchet searches.
- -i
number of iterations -
Number of iterations for each ratchet search.
- -n
number of characters -
Total number of characters in matrix.
-h-
Print help message and quit.
FILES
The program requires a valid newick-formatted labelled tree file.
SEE ALSO
Rutger Vos: http://search.cpan.org/~rvosa