2/19/2014: A related program called PIRNS is now published. It is related to
PIRN but often works faster for larger number of trees.
1/8/2013: v2.0.1: This is a new code release.
The main new
is the ability of constructing the exact most parsimonious
hybridization network for multiple rooted binary trees. Note
only for relatively small number of reticulations (specified
option). See the Readme file for more details.
PIRN is a program for reconstructing the most parsimonious
phylogenetic networks that contain
set of given phylogenetic trees. One motivation is that the
the gene trees and the phylogenetic networks model what may have
when there is horizontal gene transfer. An example of
network produced by PIRN is shown above, which contains five
trees (see the Appendix of my ISMB paper for these five trees).
main functions of PIRN is computing a lower bound on the minimum
reticulation needed and also reconstructing a network that is
close to optimum.
Note: Files can be downloaded using "Save
As..." After downloading the softwares, you may
need to change file access permissions (e.g. chmod u+x pirn).
Source code is available upon request .
Current version: v. 2.0.1. Source code
available (see below)