Software accompaniment to

Sajad Mirzaei and Yufeng Wu, " Fast Construction of Parsimonious Hybridization Networks for Multiple Phylogenetic Trees", IEEE/ACM Transaction on Computational Biology and Bioinformatics (link, preprint), accepted, 2015.

PIRNS is a program for reconstructing the most parsimonious phylogenetic networks that contain a set of given phylogenetic trees. Its goal is similar to the program PIRN. PIRNS is written in Java by Sajad Mirzaei. Contact Sajad (sajad@engr.uconn.edu) if you have questions about it.

PIRNS java executable: to run it, first download to your own machine. To run it, type: java -jar pirns.jar <input gene trees>. The gene tree file should contain only gene tree file in the Newick format. It is the same data format as PIRN. The output network is stored in a file called output.gml. It is in the GML format. See the PIRN's webpage for advice on how to view it.