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The effect of natural selection on the performance of maximum parsimony [PDF]
BMC Evolutionary Biology, 2007 Background Maximum parsimony is one of the most commonly used and extensively studied phylogeny reconstruction methods. While current evaluation methodologies such as computer simulations provide insight into how well maximum parsimony reconstructs ...
Ofria Charles +3 more
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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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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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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 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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The worst case complexity of maximum parsimony. [PDF]
J Comput Biol, 2014 Abstract One of the core classical problems in computational biology is that of constructing the most parsimonious phylogenetic tree interpreting an input set of sequences from the genomes of evolutionarily related organisms.
Carmel A +3 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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