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
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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On the computational complexity of the maximum parsimony reconciliation problem in the duplication-loss-coalescence model [PDF]
Algorithms for Molecular Biology, 2017 Ran Libeskind-Hadas +1 more
exaly +2 more sources
Phylogenetic analysis of seven WRKY genes across the palm subtribe Attaleinae (Arecaceae) [corrected] identifies Syagrus as sister group of the coconut. [PDF]
PLoS ONE, 2009 BACKGROUND:The Cocoseae is one of 13 tribes of Arecaceae subfam. Arecoideae, and contains a number of palms with significant economic importance, including the monotypic and pantropical Cocos nucifera L., the coconut, the origins of which have been one ...
Alan W Meerow +9 more
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Feasibility of nuclear ribosomal region ITS1 over ITS2 in barcoding taxonomically challenging genera of subtribe Cassiinae (Fabaceae) [PDF]
PeerJ, 2016 Premise of the Study The internal transcribed spacer (ITS) region is situated between 18S and 26S in a polycistronic rRNA precursor transcript. It had been proved to be the most commonly sequenced region across plant species to resolve phylogenetic ...
Priyanka Mishra +4 more
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BMC Bioinformatics, 2019 Background Maximum parsimony reconciliation in the duplication-transfer-loss model is widely used in studying the evolutionary histories of genes and species and in studying coevolution of parasites and their hosts and pairs of symbionts. While efficient
Santi Santichaivekin +2 more
doaj +1 more source
BMC Bioinformatics, 2019 Background Reconciliation methods are widely used to explain incongruence between a gene tree and species tree. However, the common approach of inferring maximum parsimony reconciliations (MPRs) relies on user-defined costs for each type of event, which ...
Ross Mawhorter +3 more
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Maximum likelihood models and algorithms for gene tree evolution with duplications and losses
BMC Bioinformatics, 2011 Background The abundance of new genomic data provides the opportunity to map the location of gene duplication and loss events on a species phylogeny. The first methods for mapping gene duplications and losses were based on a parsimony criterion, finding ...
Burleigh Gordon J +2 more
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Phylogenetic reconciliation. [PDF]
PLoS Comput Biol, 2022 Menet H, Daubin V, Tannier E.
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Tree Reconciliation Methods for Host-Symbiont Cophylogenetic Analyses. [PDF]
Life (Basel), 2022 Libeskind-Hadas R.
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