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Bioinformatics Advance Access published online on December 14, 2004
Bioinformatics, doi:10.1093/bioinformatics/bti208
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Bioinformatics © Oxford University Press 2004; all rights reserved.
Received September 3, 2004
Revised November 30, 2004
Accepted December 2, 2004

Applications note

GeneContent: software for whole-genome phylogenetic analysis

Xun Gu 1*, Wei Huang 2, Dongping Xu 3, and Hongmei Zhang 4

1 Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, IA 50011, USA; Center for Bioinformatics and Biological Statistics, Iowa State University, Ames, IA 50011, USA
2 Department of Electrical and Computer Engineering, Iowa State University, Ames, IA 50011, USA
3 Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, IA 50011, USA
4 Department of Mathematics and Statistics, University of West Florida, Pensacola, FL 32514, USA

* To whom correspondence should be addressed.
Xun Gu, E-mail: xgu{at}iastate.edu


  Abstract

Summary: GeneContent is a software system to infer the genome phylogeny based on an additive genome distance that can be estimated from the extended gene content data, which contains the genome-wide information (absence of a gene family, presence as single copy, or presence as duplicates) across multiple species. GeneContent can also be used to explore the genome-wide evolutionary pattern of gene loss and proliferation.

Availability: Distribution packages of GeneContent for both Microsoft Windows and Linux operating systems are available at http://xgu.zool.iastate.edu.


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