TOPD/FMTS: a new software to compare phylogenetic trees Export

@article{citeulike:1692579, 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 10.1093/bioinformatics/btm135}, author = {Puigbo, Pere and Garcia-Vallve, Santiago and McInerney, James O.}, citeulike-article-id = {1692579}, citeulike-linkout-0 = {http://dx.doi.org/10.1093/bioinformatics/btm135}, citeulike-linkout-1 = {http://bioinformatics.oxfordjournals.org/content/btm135v1/.abstract}, citeulike-linkout-2 = {http://bioinformatics.oxfordjournals.org/content/btm135v1/.full.pdf}, citeulike-linkout-3 = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/23/12/1556}, citeulike-linkout-4 = {http://view.ncbi.nlm.nih.gov/pubmed/17459965}, citeulike-linkout-5 = {http://www.hubmed.org/display.cgi?uids=17459965}, day = {25}, doi = {10.1093/bioinformatics/btm135}, issn = {1460-2059}, journal = {Bioinformatics}, keywords = {phylogenetics}, month = {April}, number = {12}, pages = {btm135--1558}, posted-at = {2009-11-09 10:02:54}, priority = {2}, title = {TOPD/FMTS: a new software to compare phylogenetic trees}, url = {http://dx.doi.org/10.1093/bioinformatics/btm135}, volume = {23}, year = {2007} }

TY - JOUR ID - citeulike:1692579 L3 - citeulike-article-id:1692579 N2 - 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 10.1093/bioinformatics/btm135 IS - 12 JF - Bioinformatics SN - 1460-2059 EP - 1558 TI - TOPD/FMTS: a new software to compare phylogenetic trees VL - 23 SP - btm135 KW - phylogenetics AU - Puigbo, Pere AU - Garcia-Vallve, Santiago AU - McInerney, James PY - 2007/04/25/ UR - http://dx.doi.org/10.1093/bioinformatics/btm135 ER -