Skip Navigation



Bioinformatics Advance Access published online on April 25, 2007
Bioinformatics, doi:10.1093/bioinformatics/btm135
This Article
Right arrow Advance Access manuscript (PDF) Freely available
Right arrow All Versions of this Article:
23/12/1556    most recent
btm135v1
Right arrow Comments: Submit a response
Right arrow Alert me when this article is cited
Right arrow Alert me when Comments are posted
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 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 Puigbò, P.
Right arrow Articles by McInerney, J. O.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Puigbò, P.
Right arrow Articles by McInerney, J. O.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© The Author (2007). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

TOPD/FMTS: a new software to compare phylogenetic trees

Pere Puigbò 1,*, Santiago Garcia-Vallvé 1 and James O. McInerney 2

1 Evolutionary Genomics Group. Biochemistry and Biotechnology Department. "Rovira i Virgili" University. Tarragona (Spain).
2 Bioinformatics Laboratory. National University of Ireland, Maynooth. Maynooth (Ireland).

*To whom correspondence should be addressed. Pere Puigbò, E-mail: ppuigbo{at}urv.cat


  Abstract

Summary: TOPD/FMTS has been developed to evaluate similarities and differences between phylogenetic trees. The software implements several new algorithms (including the Disagree method that returns the taxa that disagree between two trees and the Nodal method that compares two trees using nodal information) and several previously described methods (such as the Partition method, Triplets or Quartets) to compare phylogenetic trees. One of the novelties of this software is that the FMTS program allows the comparison of trees that contain both orthologs and paralogues. Each option is also complemented with a randomisation analysis to test the null hypothesis that the similarity between two trees is not better than chance expectation.

Availability: The Perl source code of TOPD/FMTS is available topd/fmts has been precompiled in Linux, Windows and Macintosh operating systems. It is available at http://genomes.urv.es/topd.The Perl source code is available on request to the authors.

Supplementary Information: A complete tutorial and several examples of how to use the software have been included on the home page of the application

Associate Editor: Dr. Joaquin Dopazo

Received on January 17, 2007; revised on March 16, 2007; accepted on April 2, 2007

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


This article has been cited by other articles:


Home page
 Cold Spring Harb Symp Quant BiolHome page
E.V. Koonin, Y.I. Wolf, and P. Puigbo
The Phylogenetic Forest and the Quest for the Elusive Tree of Life
Cold Spring Harb Symp Quant Biol, August 17, 2009; (2009) sqb.2009.74.006v1.
[Abstract] [PDF]


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.