An example phylogenetic

Software accompaniment to
1. Yufeng Wu, "Close lower and upper bounds for the minimum reticulate network of multiple phylogenetic trees", in Proceedings of ISMB 2010, Bioinformatics 2010 26(12):i140-i148, 2010.  Here is the preprint of this paper PDF.
2. Yufeng Wu, "An Algorithm for Constructing Parsimonious Hybridization Networks with Multiple Phylogenetic Trees", in Proceedings of RECOMB 2013. Here is the preprint of the this paper

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 feature is the ability of constructing the exact most parsimonious hybridization network for multiple rooted binary trees. Note this works only for relatively small number of reticulations (specified by -r option). See the Readme file for more details.

PIRN is a program for reconstructing the most parsimonious phylogenetic networks that contain a set of given phylogenetic trees. One motivation is that the trees are the gene trees and the phylogenetic networks model what may have happen when there is horizontal gene transfer. An example of phylogenetic network produced by PIRN is shown above, which contains five input gene trees (see the Appendix of my ISMB paper for these five trees). The main functions of PIRN is computing a lower bound on the minimum reticulation needed and also reconstructing a network that is usually close to optimum.

Note: Files can be downloaded using "Save Link/Target 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)

If you want to build from source code, please check out this link.