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Bioinformatics Advance Access originally published online on April 25, 2007
Bioinformatics 2007 23(12):1556-1558; doi:10.1093/bioinformatics/btm135
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© 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

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

*To whom correspondence should be addressed.


  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 (From Multiple to Single) program allows the comparison of trees that contain both orthologs and paralogs. Each option is also complemented with a randomization 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 at http://genomes.urv.es/topd.

Contact: ppuigbo{at}urv.cat

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: Joaquin Dopazo

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

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