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Maximum agreement and compatible supertrees

Vincent Berry, François Nicolas
2007 Journal of Discrete Algorithms  
In this paper, we propose extensions of these problems to the context of supertree inference, where input trees have non-identical leaf sets.  ...  with identical leaf sets, the MAST problem, respectively MCT problem, consists of finding a largest subset of leaves such that all input trees restricted to these leaves are isomorphic, respectively compatible  ...  A supertree compatible with T that is of maximum size is called a maximum compatible supertree of T and is denoted SMCT(T ).  ... 
doi:10.1016/j.jda.2006.08.005 fatcat:z432pbbufrgxzgv2laq6yqqvv4

Maximum Agreement and Compatible Supertrees [chapter]

Vincent Berry, François Nicolas
2004 Lecture Notes in Computer Science  
In this paper, we propose extensions of these problems to the context of supertree inference, where input trees have non-identical leaf sets.  ...  SMAST is shown to be W[2]-hard when the considered parameter is the number of input leaves that have to be removed to obtain the agreement of the input trees. A simlar result holds for SMCT.  ...  A supertree compatible with T that is of maximum size is called a maximum compatible supertree of T and is denoted SMCT (T ).  ... 
doi:10.1007/978-3-540-27801-6_15 fatcat:hchjnoadnber7feo45i55l3puu

Fixed Parameter Polynomial Time Algorithms for Maximum Agreement and Compatible Supertrees [article]

Viet Tung Hoang, Wing-Kin Sung
2008 arXiv   pre-print
In this paper, we focus on two particular supertree problems, namely, the maximum agreement supertree problem (MASP) and the maximum compatible supertree problem (MCSP).  ...  This paper gives the first polynomial time algorithms for both MASP and MCSP when both k and the maximum degree D of the trees are constant.  ...  This paper focuses on two particular supertree methods, namely the Maximum Agreement Supertree (MASP) [8] and the Maximum Compatible Supertree (MCSP) [2] .  ... 
arXiv:0802.2867v1 fatcat:gdlxa4c2gvhp7fgqrv6kcyqyaq

Fixed Parameter Polynomial Time Algorithms for Maximum Agreement and Compatible Supertrees

Viet Tung Hoang, Wing-Kin Sung, Marc Herbstritt
2008 Symposium on Theoretical Aspects of Computer Science  
In this paper, we focus on two particular supertree problems, namely, the maximum agreement supertree problem (MASP) and the maximum compatible supertree problem (MCSP).  ...  This paper gives the first polynomial time algorithms for both MASP and MCSP when both k and the maximum degree D of the trees are constant.  ...  This paper focuses on two particular supertree methods, namely the Maximum Agreement Supertree (MASP) [8] and the Maximum Compatible Supertree (MCSP) [2] .  ... 
doi:10.4230/lipics.stacs.2008.1357 dblp:conf/stacs/HoangS08 fatcat:o4uhlqf6snbd3mvpprxkt22iou

Optimal Agreement Supertrees [chapter]

David Bryant
2001 Lecture Notes in Computer Science  
The criteria of optimality can be one of four standard phylogenetic criteria: binary character compatibility; maximum summed quartet weight; ordinary least squares; and minimum evolution.  ...  In some cases, there may be no possible agreement supertrees of a set of trees, in other cases there may be exponentially many.  ...  Acknowledgements We wish to thank an anonymous referee for their helpful comments and suggestions.  ... 
doi:10.1007/3-540-45727-5_3 fatcat:2cb4tv2qenge5nlcskzwsft3vm

Comparative Performance of Supertree Algorithms in Large Data Sets Using the Soapberry Family (Sapindaceae) as a Case Study

Sven Buerki, Félix Forest, Nicolas Salamin, Nadir Alvarez
2010 Systematic Biology  
Supertree methods were evaluated using several criteria: similarity of the supertrees with the input trees, similarity between the supertrees and the total evidence tree, level of resolution of the supertree  ...  The latter would prove to be particularly useful for promising approaches such as the maximum quartet fit method that yet requires substantial computing power.  ...  ., CONCATENATE, Dquad) and help with Dquad.  ... 
doi:10.1093/sysbio/syq057 pmid:21068445 fatcat:lh2ucrwprnbljgiwlayrsitpue

Does a tree-like phylogeny only exist at the tips in the prokaryotes?

C. J. Creevey, D. A. Fitzpatrick, G. K. Philip, R. J. Kinsella, M. J. O'Connell, M. M. Pentony, S. A. Travers, M. Wilkinson, J. O. McInerney
2004 Proceedings of the Royal Society of London. Biological Sciences  
Here we use supertree methods to ask whether a definitive prokaryotic phylogenetic tree exists and whether it can be confidently inferred using orthologous genes.  ...  Deep-level prokaryotic relationships are difficult to infer because of signal erosion, systematic bias, hidden paralogy and/or HGT.  ...  Here we use supertree methods to measure agreement among gene trees and to test the hypothesis of a prokaryotic phylogenetic tree at both shallow and deeper levels.  ... 
doi:10.1098/rspb.2004.2864 pmid:15615680 pmcid:PMC1691901 fatcat:ikqdmgut5nfrtmybjiorshbdki

Using Robinson-Foulds supertrees in divide-and-conquer phylogeny estimation

Xilin Yu, Thien Le, Sarah A. Christensen, Erin K. Molloy, Tandy Warnow
2021 Algorithms for Molecular Biology  
that is related to maximum likelihood supertrees), and we prove that finding the RFS of three input trees is NP-hard.  ...  on the subsets, and then merged together using a "supertree method".  ...  We define the subsets be A ∪ P and B ∪ P , where π e = [A|B] ), and we re-estimate trees on these subsets and then combine the trees together using Exact-RFS-2.  ... 
doi:10.1186/s13015-021-00189-2 pmid:34183037 fatcat:y4gpmtrkbncq3em3bypsthmuye

Page 544 of Biological Reviews Vol. 80, Issue 4 [page]

2005 Biological Reviews  
An all-‘0° outgroup is appended and the matrix is subjected to a maximum parsimony phylogenetic analysis.  ...  Instead, in a supertree procedure, trees with overlapping sets of taxa are combined directly, obviating the need for compatible character sets.  ... 

An Application of Supertree Methods to Mammalian Mitogenomic Sequences

Véronique Campbell, François-Joseph Lapointe
2010 Evolutionary Bioinformatics  
The consensus methods produced poorly resolved consensus trees and did not perform well, except for the majority rule consensus with compatible groupings.  ...  The weighted supertree and matrix representation with parsimony methods performed equally well and were highly congruent with the model trees.  ...  We would also like to thank Antoine Lapointe and Daniel Stubbs for their programming skills and the RQCHP (Réseau Québécois de Calcul de Haute Performance) for granting access to its HPC facilities for  ... 
doi:10.4137/ebo.s4527 pmid:20535231 pmcid:PMC2880846 fatcat:2bbbjiqzojeuzofb34dnr7wrae

Rooted Maximum Agreement Supertrees

Jesper Jansson, Joseph H.-K. Ng, Kunihiko Sadakane, Wing-Kin Sung
2005 Algorithmica  
Given a set T of rooted, unordered trees, where each Ti ∈ T is distinctly leaf-labeled by a set Λ(Ti) and where the sets Λ(Ti) may overlap, the maximum agreement supertree problem (MASP) is to construct  ...  Let n = T i ∈T Λ(Ti) , k = |T |, and D = maxT i ∈T deg(Ti) .  ...  . , U is an agreement supertree of T . 1 , U is also a maximum agreement supertree of T | L.  ... 
doi:10.1007/s00453-004-1147-5 fatcat:4jculpqzzfcnpk4obc4rcpulz4

Rooted Maximum Agreement Supertrees [chapter]

Jesper Jansson, Joseph H. -K. Ng, Kunihiko Sadakane, Wing-Kin Sung
2004 Lecture Notes in Computer Science  
Given a set T of rooted, unordered trees, where each Ti ∈ T is distinctly leaf-labeled by a set Λ(Ti) and where the sets Λ(Ti) may overlap, the maximum agreement supertree problem (MASP) is to construct  ...  Let n = T i ∈T Λ(Ti) , k = |T |, and D = maxT i ∈T deg(Ti) .  ...  . , U is an agreement supertree of T . 1 , U is also a maximum agreement supertree of T | L.  ... 
doi:10.1007/978-3-540-24698-5_53 fatcat:d3yta7oxrfb7xf24wfhoqxa3xu

The evolution of supertrees

Olaf R.P. Bininda-Emonds
2004 Trends in Ecology & Evolution  
Nieselt-Struwe and Mike Steel for the invitation to attend.  ...  I thank Julia Gockel, Andy Purvis, Charles Semple, Mike Steel and four anonymous reviewers for comments that helped to improve this article.  ...  maximum fit to the set of source trees according to some OBJECTIVE FUNCTION (optimization supertrees) (Figure 1b ).  ... 
doi:10.1016/j.tree.2004.03.015 pmid:16701277 fatcat:peqsqf5evbhjjh4ai3yurqdu7e

The evolution of supertrees

O BININDAEMONDS
2004 Trends in Ecology & Evolution  
Nieselt-Struwe and Mike Steel for the invitation to attend.  ...  I thank Julia Gockel, Andy Purvis, Charles Semple, Mike Steel and four anonymous reviewers for comments that helped to improve this article.  ...  maximum fit to the set of source trees according to some OBJECTIVE FUNCTION (optimization supertrees) (Figure 1b ).  ... 
doi:10.1016/s0169-5347(04)00070-9 fatcat:x3xtx7gscjhidn2bldhdblvr4u

Minority rule supertrees? MRP, Compatibility, and Minimum Flip may display the least frequent groups

Pablo A. Goloboff
2005 Cladistics  
New examples are presented, showing that supertree methods such as matrix representation with parsimony, minimum flip trees, and compatibility analysis of the matrix representing the input trees, produce  ...  First, the measure of fit between a supertree and an input tree must be symmetrical.  ...  Olaf Bininda-Emonds acted as a reviewer of our earlier paper (Goloboff and Pol, 2002) and provided useful suggestions for improvements.  ... 
doi:10.1111/j.1096-0031.2005.00064.x fatcat:szwqn7yybfdsrlqirw5a2ly4b4
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