Split based computation of majority rule supertrees Journal Article


Author(s): Kupczok, Anne
Article Title: Split based computation of majority rule supertrees
Affiliation IST Austria
Abstract: Background Supertree methods combine overlapping input trees into a larger supertree. Here, I consider split-based supertree methods that first extract the split information of the input trees and subsequently combine this split information into a phylogeny. Well known split-based supertree methods are matrix representation with parsimony and matrix representation with compatibility. Combining input trees on the same taxon set, as in the consensus setting, is a well-studied task and it is thus desirable to generalize consensus methods to supertree methods. Results Here, three variants of majority-rule (MR) supertrees that generalize majority-rule consensus trees are investigated. I provide simple formulas for computing the respective score for bifurcating input- and supertrees. These score computations, together with a heuristic tree search minmizing the scores, were implemented in the python program PluMiST (Plus- and Minus SuperTrees) available from http://www.cibiv.at/software/plumist webcite. The different MR methods were tested by simulation and on real data sets. The search heuristic was successful in combining compatible input trees. When combining incompatible input trees, especially one variant, MR(-) supertrees, performed well. Conclusions The presented framework allows for an efficient score computation of three majority-rule supertree variants and input trees. I combined the score computation with a heuristic search over the supertree space. The implementation was tested by simulation and on real data sets and showed promising results. Especially the MR(-) variant seems to be a reasonable score for supertree reconstruction. Generalizing these computations to multifurcating trees is an open problem, which may be tackled using this framework.
Journal Title: BMC Evolutionary Biology
Volume: 11
Issue 205
ISSN: 1471-2148
Publisher: BioMed Central  
Date Published: 2011-07-13
Start Page: 1
End Page: 13
Copyright Statement: CC-BY
Sponsor: Hungarian Bioinformatics project (HuBi MTKD-CT-2006-042794), Wiener Wissenschafts-, Forschungs- and Technologiefonds (WWTF) to Arndt von Haeseler
URL:
DOI: 10.1186/1471-2148-11-205
Notes: The author likes to thank Jonathan P. Bollback for assistance in analyzing the prokaryote supertrees, Arndt von Haeseler and Bui Quang Minh for valuable comments on the manuscript and Mark Wilkinson for motivating discussions.
Open access: yes (OA journal)