Skip Navigation

Briefings in Bioinformatics 2005 6(4):394-401; doi:10.1093/bib/6.4.394
This Article
Right arrow FREE Full Text (PDF) Freely available
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in ISI Web of Science
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Li, Z.
Right arrow Articles by Zhong, Y.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Li, Z.
Right arrow Articles by Zhong, Y.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© Henry Stewart Publications

Software review

Detecting horizontal gene transfer with T-REX and RHOM programs

Zuofeng Li, Li Wang and Yang Zhong
School of Life Sciences, Fudan University, Shanghai 200433, China.


Shanghai Center for Bioinformation Technology, Shanghai 201203, China Tel: 86 21 55664436 E-mail: yangzhong{at}fudan.edu.cn

As the Human Genome Project and other genome projects experience remarkable success and a flood of biological data is produced by means of high-throughout sequencing techniques, detection of horizontal gene transfer (HGT) becomes a promising field in bioinformatics. This review describes two freeware programs: T-REX for MS Windows and RHOM for Linux. TREX is a graphical user interface program that offers functions to reconstruct the HGT network among the donor and receptor hosts from the gene and species distance matrices. RHOM is a set of command-line driven programs used to detect HGT in genomes. While TREX impresses with a user-friendly interface and drawing of the reticulation network, the strength of RHOM is an extensive statistical framework of genome and the graphical display of the estimated sequence position probabilities for the candidate horizontally transferred genes.

Keywords: horizontal gene transfer, lateral gene transfer, phylogeny, freeware


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?




Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.