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Title

HGT-Gen: a tool for generating a phylogenetic tree with horizontal gene transfer

 

Authors

Tokumasa Horiike1*, Daisuke Miyata2, Yoshio Tateno3, Ryoichi Minai1

 

Affiliation

1Division of Global Research Leaders, Shizuoka University, Shizuoka 422-8529, Japan; 2Department of Economics, Chiba University of Commerce, Ichikawa 272-8512, Japan; 3School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang, 790-784, Republic of Korea.

 

Email

dthorii@ipc.shizuoka.ac.jp; *Corresponding author

 

Article Type

Software

 

Date

Received October 06, 2011; Accepted October 24, 2011; Published October 31, 2011

 

Abstract

Horizontal gene transfer (HGT) is a common event in prokaryotic evolution. Therefore, it is very important to consider HGT in the study of molecular evolution of prokaryotes. This is true also for conducting computer simulations of their molecular phylogeny because HGT is known to be a serious disturbing factor for estimating their correct phylogeny. To the best of our knowledge, no existing computer program has generated a phylogenetic tree with HGT from an original phylogenetic tree. We developed a program called HGT-Gen that generates a phylogenetic tree with HGT on the basis of an original phylogenetic tree of a protein or gene. HGT-Gen converts an operational taxonomic unit or a clade from one place to another in a given phylogenetic tree. We have also devised an algorithm to compute the average length between any pair of branches in the tree. It defines and computes the relative evolutionary time to normalize evolutionary time for each lineage. The algorithm can generate an HGT between a pair of donor and acceptor lineages at the same evolutionary time. HGT-Gen is used with a sequence-generating program to evaluate the influence of HGT on the molecular phylogeny of prokaryotes in a computer simulation study.

 

Citation

Horiike et al. Bioinformation 7(5): 211-213 (2011)
 

Edited by

P Kangueane

 

ISSN

0973-2063

 

Publisher

Biomedical Informatics

 

Copyright

Publisher

 

Copyright Transfer Agreement

The authors of published articles in Bioinformation automatically transfer the copyright to the publisher upon formal acceptance. However, the authors reserve right to use the information contained in the article for non commercial purposes.

 

License

This is an open-access article, which permits unrestricted use, distribution, and reproduction in any medium, for non-commercial purposes, provided the original author and source are credited.