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

BMC Bioinformatics

Software

David Fernández-Baca¹  Ruchi Chaudhary¹  Oliver Eulenstein¹  André Wehe²  Mukul S Bansal³ 

[1] Department of Computer Science, Iowa State University, 50011, Ames, IA, USA;Department of Electrical and Computer Engineering, Iowa State University, 50011, Ames, IA, USA;The Blavatnik School of Computer Science, Tel Aviv University, 69978, Tel Aviv, Israel;

关键词: Species Tree;    Gene Tree;    Tree Search;    Incomplete Lineage Sorting;    Menu Item;   

DOI  :  10.1186/1471-2105-11-574

 received in 2010-07-22, accepted in 2010-11-23,  发布年份 2010

来源: Springer

【 摘 要 】

BackgroundThe 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.ResultsWe 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.ConclusionsiGTP 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.

【 授权许可】

Unknown   
© Chaudhary et al; licensee BioMed Central Ltd. 2010. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.