iGTP is a program designed to help biologists infer species phylogenies from gene phylogenies, using the gene tree parsimony (GTP) approach. The program implements efficient heuristics which allows it to handle large-scale species tree inference under the duplication, duplication-loss, and deep coalescence reconciliation costs.

iGTP provides the following features:
  • Allowing unrooted input gene trees
  • Providing three-dimensional tree visualization
  • Computing reconciliation costs
The front-end of iGTP is written in Java Swing. The programs that implement the GTP searches for the different reconciliation costs are written in C++. Paloverde is used to visualize phylogenies.

iGTP is designed as a platform independent program. It has been successfully tested on Mac OS X (10.4.11, 10.5.8), Microsoft Windows (XP, Vista, and 7), and Linux virtual box.

If you use iGTP please include the following citation:

Ruchi Chaudhary, Mukul S. Bansal, André Wehe, David Fernández-Baca, Oliver Eulenstein, "iGTP: A software package for large-scale gene tree parsimony analysis", BMC Bioinformatics 2010, 11:574.


We thank Dr. Mike Sanderson for helping in enhancing Paloverde, and Dr. J. Gordon Burleigh and Minh Anh Nguyen for their extensive testing of the software.

This work was supported in part by the NSF AToL program through grants DEB-0334832 and DEB-0829674. MSB was supported in part by a postdoctoral fellowship from the Edmond J. Safra Bioinformatics program at Tel-Aviv university.