Maximum parsimony reconciliation in the DTLOR model [PDF]
BMC Bioinformatics, 2021 Background Analyses of microbial evolution often use reconciliation methods. However, the standard duplication-transfer-loss (DTL) model does not account for the fact that species trees are often not fully sampled and thus, from the perspective of ...
Jingyi Liu +5 more
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Hierarchical clustering of maximum parsimony reconciliations [PDF]
BMC Bioinformatics, 2019 Background Maximum parsimony reconciliation in the duplication-transfer-loss model is a widely-used method for analyzing the evolutionary histories of pairs of entities such as hosts and parasites, symbiont species, and species and genes. While efficient
Ross Mawhorter, Ran Libeskind-Hadas
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Maximum Parsimony on Phylogenetic networks [PDF]
Algorithms for Molecular Biology, 2012 Background Phylogenetic networks are generalizations of phylogenetic trees, that are used to model evolutionary events in various contexts. Several different methods and criteria have been introduced for reconstructing phylogenetic trees.
Kannan Lavanya, Wheeler Ward C
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Maximum parsimony interpretation of chromatin capture experiments. [PDF]
PLoS ONE, 2019 We present a new approach to characterizing the global geometric state of chromatin from HiC data. Chromatin conformation capture techniques (3C, and its variants: 4C, 5C, HiC, etc.) probe the spatial structure of the genome by identifying physical ...
Dirar Homouz, Andrzej S Kudlicki
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MPBoot: fast phylogenetic maximum parsimony tree inference and bootstrap approximation [PDF]
BMC Evolutionary Biology, 2018 Background The nonparametric bootstrap is widely used to measure the branch support of phylogenetic trees. However, bootstrapping is computationally expensive and remains a bottleneck in phylogenetic analyses.
Diep Thi Hoang +5 more
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Protocol combining tree-based Maximum Parsimony and web-like Phylogenetic Networks analyses to investigate reticulate human evolution [PDF]
STAR Protocols, 2022 Summary: Our protocol combines Maximum Parsimony and Phylogenetic Networks approaches to understand the phylogenetic relationships and evolutionary processes of hominin species that might have shared inheritance from multiple ancestors. By addressing the
Miguel Caparros, Sandrine Prat
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PTree: pattern-based, stochastic search for maximum parsimony phylogenies [PDF]
PeerJ, 2013 Phylogenetic reconstruction is vital to analyzing the evolutionary relationship of genes within and across populations of different species. Nowadays, with next generation sequencing technologies producing sets comprising thousands of sequences, robust ...
Ivan Gregor +2 more
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Bootstrap-based Support of HGT Inferred by Maximum Parsimony [PDF]
BMC Evolutionary Biology, 2010 Background Maximum parsimony is one of the most commonly used criteria for reconstructing phylogenetic trees. Recently, Nakhleh and co-workers extended this criterion to enable reconstruction of phylogenetic networks, and demonstrated its application to ...
Nakhleh Luay, Jin Guohua, Park Hyun
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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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