Email updates

Keep up to date with the latest news and content from BMC Bioinformatics and BioMed Central.

Open Access Highly Accessed Software

iGTP: A software package for large-scale gene tree parsimony analysis

Ruchi Chaudhary1, Mukul S Bansal2, André Wehe3, David Fernández-Baca1 and Oliver Eulenstein1*

Author Affiliations

1 Department of Computer Science, Iowa State University, Ames, IA 50011, USA

2 The Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel

3 Department of Electrical and Computer Engineering, Iowa State University, Ames, IA 50011, USA

For all author emails, please log on.

BMC Bioinformatics 2010, 11:574  doi:10.1186/1471-2105-11-574

Published: 23 November 2010

Abstract

Background

The ever-increasing wealth of genomic sequence information provides an unprecedented opportunity for large-scale phylogenetic analysis. However, species phylogeny inference is obfuscated by incongruence among gene trees due to evolutionary events such as gene duplication and loss, incomplete lineage sorting (deep coalescence), and horizontal gene transfer. Gene tree parsimony (GTP) addresses this issue by seeking a species tree that requires the minimum number of evolutionary events to reconcile a given set of incongruent gene trees. Despite its promise, the use of gene tree parsimony has been limited by the fact that existing software is either not fast enough to tackle large data sets or is restricted in the range of evolutionary events it can handle.

Results

We introduce iGTP, a platform-independent software program that implements state-of-the-art algorithms that greatly speed up species tree inference under the duplication, duplication-loss, and deep coalescence reconciliation costs. iGTP significantly extends and improves the functionality and performance of existing gene tree parsimony software and offers advanced features such as building effective initial trees using stepwise leaf addition and the ability to have unrooted gene trees in the input. Moreover, iGTP provides a user-friendly graphical interface with integrated tree visualization software to facilitate analysis of the results.

Conclusions

iGTP enables, for the first time, gene tree parsimony analyses of thousands of genes from hundreds of taxa using the duplication, duplication-loss, and deep coalescence reconciliation costs, all from within a convenient graphical user interface.