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The Influence of the Number of Tree Searches on Maximum Likelihood Inference in Phylogenomics
Systematic BiologyAbstract Maximum likelihood (ML) phylogenetic inference is widely used in phylogenomics. As heuristic searches most likely find suboptimal trees, it is recommended to conduct multiple (e.g., 10) tree searches in phylogenetic analyses. However, beyond its positive role, how and to what extent multiple tree searches aid ML phylogenetic ...
Chao Liu +9 more
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Phylogenomics resolves a congruent noctuoid Tree of Life
Zoological Journal of the Linnean SocietyAbstract Noctuoidea, the most diverse and economically significant superfamily of Lepidoptera (butterflies and moths), remain phylogenetically challenging due to the superfamily’s rapid radiation during the Late Cretaceous to Palaeogene.
Yehao Wang +2 more
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Collapsing dubiously resolved gene-tree branches in phylogenomic coalescent analyses
Molecular Phylogenetics and Evolution, 2021Mark P Simmons, John Gatesy
exaly
Gene-tree misrooting drives conflicts in phylogenomic coalescent analyses of palaeognath birds
Molecular Phylogenetics and Evolution, 2022Mark P Simmons +2 more
exaly
Tree2GD: a phylogenomic method to detect large-scale gene duplication events
Bioinformatics, 2022Duoyuan Chen +2 more
exaly