Results 31 to 40 of about 47,758 (285)
On Computing the Maximum Parsimony Score of a Phylogenetic Network [PDF]
SIAM Journal on Discrete Mathematics, 2015 Phylogenetic networks are used to display the relationship of different species whose evolution is not treelike, which is the case, for instance, in the presence of hybridization events or horizontal gene transfers. Tree inference methods such as Maximum Parsimony need to be modified in order to be applicable to networks.
Fischer, Mareike +3 more
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On the Maximum Parsimony Distance Between Phylogenetic Trees [PDF]
Annals of Combinatorics, 2015 Within the field of phylogenetics there is great interest in distance measures to quantify the dissimilarity of two trees. Here, based on an idea of Bruen and Bryant, we propose and analyze a new distance measure: the Maximum Parsimony (MP) distance.
Fischer, Mareike, Kelk, Steven
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Parametric Maximum Parsimonious Reconstruction on Trees [PDF]
Bulletin of Mathematical Biology, 2010 We give a formal study of the relationships between the transition cost parameters and the generalized maximum parsimonious reconstructions of unknown (ancestral) binary character states {0,1} over a phylogenetic tree. As a main result, we show there are two thresholds λ¹n and λ⁰n , generally confounded, associated to each node n of the phylogenetic ...
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Morphology–reductive coding, full taxon sample (Maximum Parsimony).
, 2023 Morphology–reductive coding, full taxon sample (Maximum Parsimony).
Davide Pisani (2695) +4 more
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PQ, a new program for phylogeny reconstruction
BMC Bioinformatics, 2018 Background Many algorithms and programs are available for phylogenetic reconstruction of families of proteins. Methods used widely at present use either a number of distance-based principles or character-based principles of maximum parsimony or maximum ...
Dmitry Penzar +2 more
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The phylogenetic relationships of geoemydid turtles from the Eocene Messel Pit Quarry: a first assessment using methods for continuous and discrete characters [PDF]
PeerJ, 2021 The geoemydid turtles of the Eocoene Messel Pit Quarry of Hesse, Germany, are part of a rich Western European fossil record of testudinoids. Originally referred to as “Ocadia” kehreri and “Ocadia” messeliana, their systematic relationships remain unclear.
Eduardo Ascarrunz +2 more
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Reconstructing phylogenetic networks using maximum parsimony [PDF]
2005 IEEE Computational Systems Bioinformatics Conference (CSB'05), 2005 Phylogenies - the evolutionary histories of groups of organisms - are one of the most widely used tools throughout the life sciences, as well as objects of research within systematics, evolutionary biology, epidemiology, etc. Almost every tool devised to date to reconstruct phylogenies produces trees; yet it is widely understood and accepted that trees
Luay Nakhleh +3 more
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A phylogenomic appraisal of the evolutionary relationship of mycoplasmas
Genetics and Molecular Biology, 2007 Several genomes of mycoplasmas have been sequenced and here we tried to retrieve the evolutionary relationships of nine species using a phylogenomic approach.
Karla S.C. Yotoko, Sandro L. Bonatto
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Improved Maximum Parsimony Models for Phylogenetic Networks [PDF]
Systematic Biology, 2017 Phylogenetic networks are well suited to represent evolutionary histories comprising reticulate evolution. Several methods aiming at reconstructing explicit phylogenetic networks have been developed in the last two decades. In this article, we propose a new definition of maximum parsimony for phylogenetic networks that permits to model biological ...
van Iersel, Leo +2 more
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Metaheuristics for the Maximum Parsimony Problem [PDF]
Computational Intelligence and Bioinformatics / 755: Modelling, Identification, and Simulation, 2011 The Maximum Parsimony (MP) problem aims at reconstructing a phylogenetic tree from DNA sequences while minimizing the total number of genetic transformations. In this paper two different metaheuristic algorithm for finding near-optimal solutions for the MP problem are proposed: iterated local search (ILS) and simulated annealing (SA).
Karla E. Vazquez-Ortiz +1 more
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