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FINDING SMALLEST SUPERTREES UNDER MINOR CONTAINMENT

NAOMI NISHIMURA, PRABHAKAR RAGDE, DIMITRIOS M THILIKOS
2000 International Journal of Foundations of Computer Science  
We consider supertrees under the general mapping of minor containment.  ...  In the simplest case, a supertree will contain exact copies of each input tree, so that for each input tree, each v ertex of a tree can be mapped to a vertex in the supertree such that each edge maps to  ...  In this paper we consider the problem of nding the smallest common supertree under minor containment.  ... 
doi:10.1142/s0129054100000259 fatcat:zwhote7gnvdzrn65otmkw5whmq

Finding Smallest Supertrees Under Minor Containment [chapter]

Naomi Nishimura, Prabhakar Ragde, Dimitrios M. Thilikos
1999 Lecture Notes in Computer Science  
We consider supertrees under the general mapping of minor containment.  ...  In the simplest case, a supertree will contain exact copies of each input tree, so that for each input tree, each vertex of a tree can be mapped to a vertex in the supertree such that each edge maps to  ...  In this paper we consider the problem of nding the smallest common supertree under minor containment.  ... 
doi:10.1007/3-540-46784-x_29 fatcat:s7lfszffirhn3fgtpntcwasp6q

Page 5286 of Mathematical Reviews Vol. , Issue 2001H [page]

2001 Mathematical Reviews  
“We consider supertrees under the general mapping of minor containment.  ...  .| (E-UPB-LI; Barcelona) Finding smallest supertrees under minor containment. (English summary) Selected papers from the Workshop on Theoretical Aspects of Computer Science (WG 99), Part 1 (Ascona).  ... 

An algebraic view of the relation between largest common subtrees and smallest common supertrees

Francesc Rosselló, Gabriel Valiente
2006 Theoretical Computer Science  
one to obtain a largest common subtree of two trees from a smallest common supertree of them, and vice versa.  ...  The relationship between two important problems in tree pattern matching, the largest common subtree and the smallest common supertree problems, is established by means of simple constructions, which allow  ...  Largest common subtree is the problem of finding a largest tree that can be embedded in two given trees, while smallest common supertree is the dual problem of finding a smallest tree into which two given  ... 
doi:10.1016/j.tcs.2006.05.031 fatcat:qzioj2y3obcu5dvnknqje7dviy

An Algebraic View of the Relation between Largest Common Subtrees and Smallest Common Supertrees [article]

Francesc Rossello, Gabriel Valiente
2006 arXiv   pre-print
one to obtain a largest common subtree of two trees from a smallest common supertree of them, and vice versa.  ...  The relationship between two important problems in tree pattern matching, the largest common subtree and the smallest common supertree problems, is established by means of simple constructions, which allow  ...  Largest common subtree is the problem of finding a largest tree that can be embedded in two given trees, while smallest common supertree is the dual problem of finding a smallest tree into which two given  ... 
arXiv:cs/0604108v1 fatcat:iutl6tppzzb4bgpnffrw7eqx5i

Majority-Rule Supertrees

James A. Cotton, Mark Wilkinson, Mike Steel
2007 Systematic Biology  
The majority-rule consensus tree is the strict consensus of the median trees under the symmetric-difference metric, so we can generalize the consensus method by generalizing this metric to trees with differing  ...  Although the supertree problem remains difficult, one promising avenue is to develop from better understood consensus methods to the more general supertree setting.  ...  supertrees at the DI-MACS 2003 meeting on bioconsensus.  ... 
doi:10.1080/10635150701416682 pmid:17558966 fatcat:qydt4gzlo5fallslhbz3exdn44

A species-level phylogenetic supertree of marsupials

Marcel Cardillo, Olaf R. P. Bininda-Emonds, Elizabeth Boakes, Andy Purvis
2004 Journal of Zoology  
One solution is to combine algorithmically many small trees into a single, larger supertree.  ...  There are also important differences in supertrees based on source phylogenies published before 1995 and those published more recently.  ...  thanks to Jon Bielby for help with collecting source trees; to Kate Jones, Rich Grenyer, Samantha Price, John Gittleman and Mike Habib for contributing to the source tree protocol and discussions about supertree  ... 
doi:10.1017/s0952836904005539 fatcat:jnpdfcyzzzhhrcfemedgtagk3m

The Complexity of Inferring a Minimally Resolved Phylogenetic Supertree [chapter]

Jesper Jansson, Richard S. Lemence, Andrzej Lingas
2010 Lecture Notes in Computer Science  
., 10 (1981), pp. 405-421] forms the basis for many modern rooted supertree methods employed in Phylogenetics.  ...  Phylogenetic Analysis, Ph.D. thesis, University of Canterbury, Christchurch, New Zealand, 1997], the tree output by the algorithm of Aho et al. is not always minimal; there may exist other trees which contain  ...  On the other hand, by definition, any minimally resolved supertree for R must be minor-minimal, so one way to solve MinRS is by running ALL-MIN-TREES to find all minor-minimal trees and then selecting  ... 
doi:10.1007/978-3-642-15294-8_22 fatcat:knwwsjet6bgvvhtehbyug6jblu

A Bayesian Supertree Model for Genome-Wide Species Tree Reconstruction

Leonardo De Oliveira Martins, Diego Mallo, David Posada
2014 Systematic Biology  
Our Bayesian supertree method was also very successful in obtaining better estimates of gene trees, by reducing the uncertainty in their distributions.  ...  Our method ranked best under simulated data sets, in spite of ignoring branch lengths, and performed well on empirical data, as well as being fast enough to analyze relatively large data sets.  ...  Under the supertree umbrella, some methods try to find the species tree that minimizes its overall disagreement with the gene tree collection without explicitly-taking into account the biological phenomena  ... 
doi:10.1093/sysbio/syu082 pmid:25281847 pmcid:PMC4851173 fatcat:posipbhcx5gshntsepnkup3tya

Finding Largest Subtrees and Smallest Supertrees

A. Gupta, N. Nishimura
1998 Algorithmica  
tree in which e a c h o f T and T 0 can be embedded (or a smallest supertree).  ...  For example, when each of the two trees contains partial information about a data set, such a s t h e e v olution of a set of species, the subtree or supertree corresponds to a structuring of the data  ...  Acknowledgements We are grateful to Ernst Mayr for pointers to references on weighted bipartite matching, and to Jianghai Fu for bringing to our attention the work of Jiang, Wang, and Zhang and the subject of supertrees  ... 
doi:10.1007/pl00009212 fatcat:lgei5tprhjchzgpj3s5esupy5m

Gene and genome trees conflict at many levels

L. S. Haggerty, F. J. Martin, D. A. Fitzpatrick, J. O. McInerney
2009 Philosophical Transactions of the Royal Society of London. Biological Sciences  
An Excel spreadsheet containing the input trees and their score against the dfit supertree can be found in the electronic supplementary material.  ...  We did not find that the three groups were a single homogenous entity; we did find partitions. There were clear boundaries, and none of our analysis methods broke these boundaries.  ... 
doi:10.1098/rstb.2009.0042 pmid:19571241 pmcid:PMC2873008 fatcat:zlh4dgb47rhankqookwhcph7ie

Reconstructing (Super)Trees from Data Sets with Missing Distances: Not All Is Lost

George Kettleborough, Jo Dicks, Ian N. Roberts, Katharina T. Huber
2015 Molecular biology and evolution  
One key problem is finding effective strategies to deal with missing data.  ...  Furthermore, by formulating the supermatrix problem as a particular case of the missing data problem, we assessed LASSO's ability to reconstruct supertrees.  ...  Acknowledgments The authors gratefully acknowledge Lesley Boyd (NIAB, Cambridge, UK) and Muge Sayar-Turet (Bogazici University, Bebek-Istanbul, Turkey) for providing a wheat data set used within the supertree  ... 
doi:10.1093/molbev/msv027 pmid:25657329 fatcat:rjlklyzz55fkbgwzf7ze7ogxea

Nudivirus Genomics and Phylogeny [chapter]

Yongjie Wang, Olaf R.P., Johannes A.
2012 Viral Genomes - Molecular Structure, Diversity, Gene Expression Mechanisms and Host-Virus Interactions  
Thus far, the smallest nudivirus genome sequenced is GbNV, which is 96,944 bp in length with a G+C content of 28% and contains 98 ORFs.  ...  For the supertree analyses, phylogenetic analyses of the individual gene trees were performed under a maximum likelihood (ML) framework using RAxML 7.0.4 (Stamatakis, Hoover and Rougemont 2008) .  ... 
doi:10.5772/27793 fatcat:ylkd75hed5b7xpugc2xf6zfygi

Tradeoff between robustness and elaboration in carotenoid networks produces cycles of avian color diversification

Alexander V. Badyaev, Erin S. Morrison, Virginia Belloni, Michael J. Sanderson
2015 Biology Direct  
Of our 152 taxa under our study, only seven (4.6 %) come from these orders. Given this minor difference and for the reasons specified above, we retained the Hackett et al.  ...  In contrast, rapid metabolic diversification Fig. 2 Distinct topologies of molecular-based supertree (left) and the metabolic pathway-based supertree (right) for species under this study.  ...  References to phylogenies used to hierarchically build the topology of the supertree. (PDF 150 kb) Competing interests The authors declare that they have no competing interests.  ... 
doi:10.1186/s13062-015-0073-6 pmid:26289047 pmcid:PMC4545997 fatcat:a422ozdnwbeptprlqouys7akx4

Genus-level supertree of Cyprinidae (Actinopterygii: Cypriniformes), partitioned qualitative clade support and test of macro-evolutionary scenarios

Philippe Gaubert, Gael Denys, Thierry Oberdorff
2009 Biological Reviews  
Contribution to the knowledge of leuciscine fishes of Asia Minor. Part 2.  ...  Measuring support and finding unsupported relationships in 2005a). The shape of supertrees. Systematic Biology 54, 823-831. WILLson, S.J. distances. Bulletin of Mathematical Biology 66, 1755-1783.  ... 
doi:10.1111/j.1469-185x.2009.00091.x pmid:19857213 fatcat:jhj33kdqvbah7is7tghl26cabm
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