Results 11 to 20 of about 47,758 (285)
Maximum parsimony on subsets of taxa [PDF]
Journal of Theoretical Biology, 2009 In this paper we investigate mathematical questions concerning the reliability (reconstruction accuracy) of Fitch's maximum parsimony algorithm for reconstructing the ancestral state given a phylogenetic tree and a character. In particular, we consider the question whether the maximum parsimony method applied to a subset of taxa can reconstruct the ...
Mareike Fischer
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MapGL: inferring evolutionary gain and loss of short genomic sequence features by phylogenetic maximum parsimony [PDF]
BMC Bioinformatics, 2020 Background Comparative genomics studies are growing in number partly because of their unique ability to provide insight into shared and divergent biology between species. Of particular interest is the use of phylogenetic methods to infer the evolutionary
Adam G. Diehl, Alan P. Boyle
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Maximum Parsimony and the Skewness Test: A Simulation Study of the Limits of Applicability. [PDF]
PLoS ONE, 2016 The maximum parsimony (MP) method for inferring phylogenies is widely used, but little is known about its limitations in non-asymptotic situations. This study employs large-scale computations with simulated phylogenetic data to estimate the probability ...
Jussi Määttä, Teemu Roos
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Non-hereditary Maximum Parsimony trees [PDF]
Journal of Mathematical Biology, 2011 In this paper, we investigate a conjecture by von Haeseler concerning the Maximum Parsimony method for phylogenetic estimation, which was published by the Newton Institute in Cambridge on a list of open phylogenetic problems in 2007. This conjecture deals with the question whether Maximum Parsimony trees are hereditary.
Mareike Fischer, Fischer Mareike
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Direct maximum parsimony phylogeny reconstruction from genotype data [PDF]
BMC Bioinformatics, 2007 Background Maximum parsimony phylogenetic tree reconstruction from genetic variation data is a fundamental problem in computational genetics with many practical applications in population genetics, whole genome analysis, and the search for genetic ...
Ravi R +4 more
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Phylogenetic relationships of Neogene hamsters (Mammalia, Rodentia, Cricetinae) revealed under Bayesian inference and maximum parsimony [PDF]
PeerJThere is an ongoing debate about the internal systematics of today’s group of hamsters (Cricetinae), following new insights that are gained based on molecular data.
Moritz Dirnberger +2 more
doaj +3 more sources
An Approximation Algorithm for Haplotype Inference by Maximum Parsimony [PDF]
Journal of Computational Biology, 2005 This paper studies haplotype inference by maximum parsimony using population data. We define the optimal haplotype inference (OHI) problem as given a set of genotypes and a set of related haplotypes, find a minimum subset of haplotypes that can resolve all the genotypes.
Yao-Ting Huang, Kun-Mao Chao
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Revisiting an Equivalence Between Maximum Parsimony and Maximum Likelihood Methods in Phylogenetics [PDF]
Bulletin of Mathematical Biology, 2009 Tuffley and Steel (1997) proved that Maximum Likelihood and Maximum Parsimony methods in phylogenetics are equivalent for sequences of characters under a simple symmetric model of substitution with no common mechanism. This result has been widely cited ever since.
Mareike Fischer, Fischer Mareike
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On the quirks of maximum parsimony and likelihood on phylogenetic networks [PDF]
Journal of Theoretical Biology, 2017 Maximum parsimony is one of the most frequently-discussed tree reconstruction methods in phylogenetic estimation. However, in recent years it has become more and more apparent that phylogenetic trees are often not sufficient to describe evolution accurately.
Mareike Fischer +2 more
exaly +5 more sources
Progressive Tree Neighborhood applied to the Maximum Parsimony Problem [PDF]
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2008 The Maximum Parsimony (MP) problem aims at reconstructing a phylogenetic tree from DNA sequences while minimizing the number of genetic transformations. To solve this NP-complete problem, heuristic methods have been developed, often based on local search. In this article, we focus on the influence of the neighborhood relations.
Goëffon, Adrien +2 more
openaire +4 more sources