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Citation for Study 1902

Citation title: "PhySIC: a veto supertree method with desirable properties.".

This study was previously identified under the legacy study ID S1879 (Status: Published).

Citation

Ranwez V., Berry V., Criscuolo A., Fabre P., Guillemot S., Scornavacca C., & Douzery E. 2007. PhySIC: a veto supertree method with desirable properties. Systematic Biology, 56(5): 798-817.

Authors

• Ranwez V.
• Berry V.
• Criscuolo A.
• Fabre P.
• Guillemot S.
• Scornavacca C.
• Douzery E.

Abstract

This paper focuses on veto supertree methods, i.e., methods that aim at producing a conservative synthesis of the relationships agreed upon by all source trees. We propose desirable properties that a supertree should satisfy in this framework, namely the non-contradiction property (PC) and the induction property (PI). The former requires that the supertree does not contain relationships that contradict one or a combination of the source topologies, whereas the latter requires that all topological information contained in the supertree is present in a source tree or collectively induced by several source trees. We provide simple examples to illustrate their relevance and that allow a comparison with previously advocated properties. We show that these properties can be checked in polynomial time for any given rooted supertree. Moreover,we introduce the PhySIC method (PHYlogenetic Signal with Induction and non-Contradiction). For k input trees spanning a set of n taxa, this method produces a supertree that satisfies the above-mentioned properties in O(kn3 + n4) polynomial computing time. The polytomies of the produced supertree are also tagged by labels indicating areas of conflict as well as those with insufficient overlap. As a whole, PhySIC enables the user to quickly summarize consensual information of a set of trees and localize groups of taxa for which the data requires consolidation. Lastly, we illustrate the behaviour of PhySIC on primate datasets of various sizes, and propose a supertree covering 95% of all primate extant genera. The PhySIC algorithm is available at http://atgc.lirmm.fr/cgi-bin/PhySIC/physic.cgi. [formal properties; phylogenetics; polynomial-time algorithms; primates; software; supertrees; triplets; veto methods.]

External links

• DOI: 10.1080/10635150701639754

About this resource

• Canonical resource URI: http://purl.org/phylo/treebase/phylows/study/TB2:S1902
• Other versions: Nexus NeXML
• Show BibTeX reference

  		@ARTICLE{TreeBASE2Ref17158,
  	 author = {Vincent  Ranwez and Vincent  Berry and Alexis  Criscuolo and P. H.  Fabre and Sylvain  Guillemot and C?line  Scornavacca and Emmanuel J. P.  Douzery},
  	 title = {PhySIC: a veto supertree method with desirable properties.},
  	 year = {2007},
  	 keywords = {},
  	 doi = {10.1080/10635150701639754},
  	 url = {},
  	 pmid = {},
  	 journal = {Systematic Biology},
  	 volume = {56},
  	 number = {5},
  	 pages = {798--817},
  	 abstract = {This paper focuses on veto supertree methods, i.e., methods that aim at producing a conservative synthesis of the relationships agreed upon by all source trees. We propose desirable properties that a supertree should satisfy in this framework, namely the non-contradiction property (PC) and the induction property (PI). The former requires that the supertree does not contain relationships that contradict one or a combination of the source topologies, whereas the latter requires that all topological information contained in the supertree is present in a source tree or collectively induced by several source trees. We provide simple examples to illustrate their relevance and that allow a comparison with previously advocated properties. We show that these properties can be checked in polynomial time for any given rooted supertree. Moreover,we introduce the PhySIC method (PHYlogenetic Signal with Induction and non-Contradiction). For k input trees spanning a set of n taxa, this method produces a supertree that satisfies the above-mentioned properties in O(kn3 + n4) polynomial computing time. The polytomies of the produced supertree are also tagged by labels indicating areas of conflict as well as those with insufficient overlap. As a whole, PhySIC enables the user to quickly summarize consensual information of a set of trees and localize groups of taxa for which the data requires consolidation. Lastly, we illustrate the behaviour of PhySIC on primate datasets of various sizes, and propose a supertree covering 95% of all primate extant genera. The PhySIC algorithm is available at http://atgc.lirmm.fr/cgi-bin/PhySIC/physic.cgi. [formal properties; phylogenetics; polynomial-time algorithms; primates; software; supertrees; triplets; veto methods.]}
  }
  		

• Show RIS reference

  		TY  - JOUR
  ID  - 17158
  AU  - Ranwez,Vincent 
  AU  - Berry,Vincent 
  AU  - Criscuolo,Alexis 
  AU  - Fabre,P. H. 
  AU  - Guillemot,Sylvain 
  AU  - Scornavacca,C?line 
  AU  - Douzery,Emmanuel J. P. 
  T1  - PhySIC: a veto supertree method with desirable properties.
  PY  - 2007
  KW  - 
  UR  - http://dx.doi.org/10.1080/10635150701639754
  N2  - This paper focuses on veto supertree methods, i.e., methods that aim at producing a conservative synthesis of the relationships agreed upon by all source trees. We propose desirable properties that a supertree should satisfy in this framework, namely the non-contradiction property (PC) and the induction property (PI). The former requires that the supertree does not contain relationships that contradict one or a combination of the source topologies, whereas the latter requires that all topological information contained in the supertree is present in a source tree or collectively induced by several source trees. We provide simple examples to illustrate their relevance and that allow a comparison with previously advocated properties. We show that these properties can be checked in polynomial time for any given rooted supertree. Moreover,we introduce the PhySIC method (PHYlogenetic Signal with Induction and non-Contradiction). For k input trees spanning a set of n taxa, this method produces a supertree that satisfies the above-mentioned properties in O(kn3 + n4) polynomial computing time. The polytomies of the produced supertree are also tagged by labels indicating areas of conflict as well as those with insufficient overlap. As a whole, PhySIC enables the user to quickly summarize consensual information of a set of trees and localize groups of taxa for which the data requires consolidation. Lastly, we illustrate the behaviour of PhySIC on primate datasets of various sizes, and propose a supertree covering 95% of all primate extant genera. The PhySIC algorithm is available at http://atgc.lirmm.fr/cgi-bin/PhySIC/physic.cgi. [formal properties; phylogenetics; polynomial-time algorithms; primates; software; supertrees; triplets; veto methods.]
  L3  - 10.1080/10635150701639754
  JF  - Systematic Biology
  VL  - 56
  IS  - 5
  SP  - 798
  EP  - 817
  ER  -