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An Optimal Algorithm for Building the Majority Rule Consensus Tree [chapter]

Jesper Jansson, Chuanqi Shen, Wing-Kin Sung
2013 Lecture Notes in Computer Science  
A deterministic algorithm for building the majority rule consensus tree of an input collection of conflicting phylogenetic trees with identical leaf labels is presented.  ...  Its worst-case running time is O(nk), where n is the size of the leaf label set and k is the number of input phylogenetic trees. This is optimal since the input size is Ω(nk).  ...  An Optimal Algorithm for the Majority Rule Consensus Tree This eliminates those candidates that do not occur in more than k 2 of the trees in S.  ... 
doi:10.1007/978-3-642-37195-0_8 fatcat:oimobmc3djabdoxch2klsi3wa4

Inferring explicit weighted consensus networks to represent alternative evolutionary histories

Mehdi Layeghifard, Pedro R Peres-Neto, Vladimir Makarenkov
2013 BMC Evolutionary Biology  
Methods: To tackle this problem, we hereby describe a new method for inferring and representing alternative (reticulate) evolutionary histories of species as an explicit weighted consensus network which  ...  Conclusions: Our weighted consensus network inference method allows one to infer, visualize and validate statistically major conflicting signals induced by the mechanisms of reticulate evolution.  ...  Acknowledgments This study was supported by the FQRNT (Fonds de Recherche sur la Nature et les Technologies du Québec) team research grant to V. Makarenkov  ... 
doi:10.1186/1471-2148-13-274 pmid:24359207 pmcid:PMC3898054 fatcat:pcakrdp3xngizlngbn3xlktvwe

Multipolar Consensus for Phylogenetic Trees

Cécile Bonnard, Vincent Berry, Nicolas Lartillot, Roderic Page
2006 Systematic Biology  
However, in the case of heterogeneous collections of trees, the resulting consensus may be poorly resolved (strict consensus, majority-rule consensus...), or may perform arbitrary choices among mutually  ...  Collections of phylogenetic trees are usually summarized using consensus methods. These methods build a single tree, supposed to be representative of the collection.  ...  Acknowledgment We thank Li-Shang Wang for providing us with the data sets used in Stockham et al. (2002) , as well Hervé Philippe, Nicolas Rodrigue, and the three referees for their useful comments on  ... 
doi:10.1080/10635150600969880 pmid:17060203 fatcat:ohgglsksxjdchlxvavly4bni3u

Online Consensus and Agreement of Phylogenetic Trees [chapter]

Tanya Y. Berger-Wolf
2004 Lecture Notes in Computer Science  
Consensus and agreement trees are common such representations. Using existing static algorithms to produce these trees increases an already lengthy computational time substantially.  ...  In this paper we present efficient online algorithms for computing strict and majority consensi and the maximum agreement subtree.  ...  The author is deeply grateful to Tandy Warnow for suggesting the problem and for many insights.  ... 
doi:10.1007/978-3-540-30219-3_30 fatcat:st23urbytje75ilcgbm5vumuwi

Polynomial-Time Algorithms for Building a Consensus MUL-Tree

Yun Cui, Jesper Jansson, Wing-Kin Sung
2012 Journal of Computational Biology  
for building a majority rule consensus MUL-tree for the special case where every leaf label occurs at most twice.  ...  We also show that, although it is NP-hard to find a majority rule consensus MUL-tree in general, the variant that we call the singular majority rule consensus MUL-tree can be constructed efficiently whenever  ...  ACKNOWLEDGMENTS Jesper Jansson was funded by The Hakubi Project at Kyoto University and KAKENHI grant number 23700011.  ... 
doi:10.1089/cmb.2012.0008 pmid:22963134 pmcid:PMC3440012 fatcat:cztggolkcrbq7fizwd5vyikyvu

Parallel computation of phylogenetic consensus trees

Andre J. Aberer, Nicholas D. Pattengale, Alexandros Stamatakis
2010 Procedia Computer Science  
In this paper we focus on a post-analysis task in reconstructing very large trees, specifically the step of building (extended) majority rules consensus trees from a collection of equally plausible trees  ...  In the field of phylogenetic inference (reconstruction of evolutionary trees from molecular sequence data), scalability is becoming an increasingly important issue for operations other than the tree reconstruction  ...  The majority rules (MR) consensus tree consists of the bipartitions that occur in more than half of the input trees.  ... 
doi:10.1016/j.procs.2010.04.118 fatcat:7qw3jrs6yvavbizpmhp4cdei6y

Improved Algorithms for Constructing Consensus Trees [chapter]

Jesper Jansson, Chuanqi Shen, Wing-Kin Sung
2013 Proceedings of the Twenty-Fourth Annual ACM-SIAM Symposium on Discrete Algorithms  
Many different types of consensus trees have been proposed in the literature; three of the most well-known and widely used ones are the majority rule consensus tree, the loose consensus tree, and the greedy  ...  Given k phylogenetic trees with n leaves each and with identical leaf label sets, our algorithms run in O(nk log k) time (majority rule consensus tree), O(nk) time (loose consensus tree), and O(n 2 k)  ...  Acknowledgments The authors would like to thank Joseph Felsenstein for clarifications regarding PHYLIP and Todd Wareham for confirming the time complexity of the deterministic algorithm in [27] .  ... 
doi:10.1137/1.9781611973105.129 dblp:conf/soda/JanssonSS13 fatcat:kwzizdo64bflfk4tujqmjvyvee

Improved Algorithms for Constructing Consensus Trees

Jesper Jansson, Chuanqi Shen, Wing-Kin Sung
2016 Journal of the ACM  
Many different types of consensus trees have been proposed in the literature; three of the most well-known and widely used ones are the majority rule consensus tree, the loose consensus tree, and the greedy  ...  Given k phylogenetic trees with n leaves each and with identical leaf label sets, our algorithms run in O(nk log k) time (majority rule consensus tree), O(nk) time (loose consensus tree), and O(n 2 k)  ...  Acknowledgments The authors would like to thank Joseph Felsenstein for clarifications regarding PHYLIP and Todd Wareham for confirming the time complexity of the deterministic algorithm in [27] .  ... 
doi:10.1145/2925985 fatcat:o4qh4fglljegnjb2bzke3jrjt4

Constructing majority-rule supertrees

Jianrong Dong, David Fernández-Baca, FR McMorris
2010 Algorithms for Molecular Biology  
Recently, Cotton and Wilkinson proposed extensions of the majority-rule consensus tree method to the supertree setting that inherit many of the appealing properties of the former.  ...  After proving that a key underlying problem for constructing majority-rule (+) supertrees is NP-hard, we develop a polynomial-size exact integer linear programming formulation of the problem.  ...  Acknowledgements The authors benefited greatly from discussions with James Cotton, William HE Day, RC Powers, and Mark Wilkinson. We thank Frédéric Delsuc for providing us the data set from [33] .  ... 
doi:10.1186/1748-7188-5-2 pmid:20047658 pmcid:PMC2826330 fatcat:h3ylyqj3xze7hhqu33byly4kce

Algorithms for the Majority Rule (+) Consensus Tree and the Frequency Difference Consensus Tree [chapter]

Jesper Jansson, Chuanqi Shen, Wing-Kin Sung
2013 Lecture Notes in Computer Science  
Given an input of k phylogenetic trees with identical leaf label sets and n leaves each, the first algorithm constructs the majority rule (+) consensus tree in O(kn) time, which is optimal since the input  ...  This paper presents two new deterministic algorithms for constructing consensus trees.  ...  Constructing the Majority Rule (+) Consensus Tree This section presents an algorithm named Maj Rule Plus for computing the majority rule (+) consensus tree of S in (optimal) O(kn) time.  ... 
doi:10.1007/978-3-642-40453-5_12 fatcat:e3whthhpsngsphoybo4tgqxvfa

Algorithms for the Majority Rule (+) Consensus Tree and the Frequency Difference Consensus Tree [article]

Jesper Jansson, Chuanqi Shen, Wing-Kin Sung
2013 arXiv   pre-print
Given an input of k phylogenetic trees with identical leaf label sets and n leaves each, the first algorithm constructs the majority rule (+) consensus tree in O(kn) time, which is optimal since the input  ...  This paper presents two new deterministic algorithms for constructing consensus trees.  ...  The situation for the frequency difference consensus tree is less critical as there already exist implementations, e.g., in the software package TNT [15] .  ... 
arXiv:1307.7821v2 fatcat:oca2vf6qazabvlq5xy7godgsvq

The metapopulation genetic algorithm: An efficient solution for the problem of large phylogeny estimation

A. R. Lemmon, M. C. Milinkovitch
2002 Proceedings of the National Academy of Sciences of the United States of America  
Here, we report on a heuristic approach, the metapopulation genetic algorithm, involving several populations of trees that are forced to cooperate in the search for the optimal tree.  ...  Within each population, trees are subjected to evaluation, selection, and mutation events, which are directed by using inter-population consensus information.  ...  This work was supported by the National Fund for Scientific Research Belgium (FNRS), the Free University of Brussels (ULB), the ''Communauté Française de Belgique'' (Grant ARC 98͞03-223), and the Van Buuren  ... 
doi:10.1073/pnas.162224399 pmid:12142465 pmcid:PMC124960 fatcat:5sfwb7nlnvad5nyk4k5pitcdza

Constructing Majority-Rule Supertrees [chapter]

Jianrong Dong, David Fernández-Baca, F. R. McMorris
2009 Lecture Notes in Computer Science  
Recently, Cotton and Wilkinson proposed extensions of the majority-rule consensus tree method to the supertree setting that inherit many of the appealing properties of the former.  ...  After proving that a key underlying problem for constructing majority-rule (+) supertrees is NP-hard, we develop a polynomial-size exact integer linear programming formulation of the problem.  ...  Acknowledgements The authors benefited greatly from discussions with James Cotton, William HE Day, RC Powers, and Mark Wilkinson. We thank Frédéric Delsuc for providing us the data set from [33] .  ... 
doi:10.1007/978-3-642-04241-6_7 fatcat:fxzr7ocvljezdbeiyoz5hcmpsy

A new fast method for inferring multiple consensus trees using k-medoids

Nadia Tahiri, Matthieu Willems, Vladimir Makarenkov
2018 BMC Evolutionary Biology  
The traditional consensus approach yields a single consensus tree. We use the popular k-medoids partitioning algorithm to divide a given set of trees into several clusters of trees.  ...  Results: We describe a new fast method for inferring multiple consensus trees from a given set of phylogenetic trees (i.e. additive trees or X-trees) defined on the same set of species (i.e. objects or  ...  These trees, studied in our article, are available in the github folder trees. Competing interests The authors declare that they have no competing interests.  ... 
doi:10.1186/s12862-018-1163-8 pmid:29621975 pmcid:PMC5887197 fatcat:cnlbugf2y5bzbptz34ni3wr5vi

Consensus Decision Trees: Using Consensus Hierarchical Clustering for Data Relabelling and Reduction [chapter]

Branko Kavšek, Nada Lavrač, Anuška Ferligoj
2001 Lecture Notes in Computer Science  
In data analysis, induction of decision trees serves two main goals: first, induced decision trees can be used for classification/prediction of new instances, and second, they represent an easyto-interpret  ...  model of the problem domain that can be used for explanation.  ...  Thanks to Saso Džeroski, Ljupčo Todorovski and Marko Grobelnik for useful comments on the draft of this paper. Thanks also to Bernard  ... 
doi:10.1007/3-540-44795-4_22 fatcat:eux7wfwi25eevaxgoxkee2ksoi
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