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Advanced Search Results For "Phylogenetics"

1 - 10 of 21,765 results for
 "Phylogenetics"
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Efficient Coalescent Epoch Model for Bayesian Phylogenetic Inference.

Publication Type: Academic Journal

Source(s): Systematic Biology. Nov2022, Vol. 71 Issue 6, p1549-1560. 12p.

Abstract: We present a two-headed approach called Bayesian Integrated Coalescent Epoch PlotS (BICEPS) for efficient inference of coalescent epoch models. Firstly, we integrate out population size parameters, and secondly, we introduce a set of more powerful Mark...

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Comparing Partitioned Models to Mixture Models: Do Information Criteria Apply?

Publication Type: Academic Journal

Source(s): Systematic Biology. Nov2022, Vol. 71 Issue 6, p1541-1548. 8p.

Abstract: The use of information criteria to distinguish between phylogenetic models has become ubiquitous within the field. However, the variety and complexity of available models are much greater now than when these practices were established. The literature s...

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Family–level phylogeny of infraorder Systellognatha (Insecta: Plecoptera) inferred from mitochondrial genomes.

Publication Type: Academic Journal

Source(s): Zoologica Scripta. Sep2022, Vol. 51 Issue 5, p589-602. 14p.

Abstract: Systellognatha is a monophyletic group within stoneflies containing seven families in two superfamilies. However, the family–level phylogeny within Systellognatha is largely unresolved, with some controversial hypotheses generated by molecular data. In...

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Extensive genome introgression between domestic ferret and European polecat during population recovery in Great Britain.

Publication Type: Academic Journal

Source(s): Journal of Heredity. Sep2022, Vol. 113 Issue 5, p500-515. 16p.

Abstract: The European polecat (Mustela putorius) is a mammalian predator which occurs across much of Europe east to the Ural Mountains. In Great Britain, following years of persecution the range of the European polecat contracted and by the early 1900s was rest...

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A class of identifiable phylogenetic birth-death models.

Publication Type: Academic Journal

Source(s): Proceedings of the National Academy of Sciences of the United States of America. 8/30/2022, Vol. 119 Issue 35, p1-10. 10p.

Abstract: In a striking result, Louca and Pennell [S. Louca, M.W. Pennell, Nature 580, 502-505 (2020)] recently proved that a large class of phylogenetic birth-death models is statistically unidentifiable from lineage-through-time (LTT) data: Any pair of suffici...

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Combining biomarker and virus phylogenetic models improves HIV-1 epidemiological source identification.

Publication Type: Academic Journal

Source(s): PLoS Computational Biology. 8/26/2022, Vol. 18 Issue 8, p1-25. 25p. 1 Color Photograph, 2 Charts, 7 Graphs.

Abstract: To identify and stop active HIV transmission chains new epidemiological techniques are needed. Here, we describe the development of a multi-biomarker augmentation to phylogenetic inference of the underlying transmission history in a local population. H...

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Evolutionary jumps in bacterial GC content.

Publication Type: Academic Journal

Source(s): G3: Genes | Genomes | Genetics. Aug2022, Vol. 12 Issue 8, p1-13. 13p.

Abstract: Genomic GC (Guanine-Cytosine) content is a fundamental molecular trait linked with many key genomic features such as codon and amino acid use. Across bacteria, GC content is surprisingly diverse and has been studied for many decades; yet its evolution ...

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J-SPACE: a Julia package for the simulation of spatial models of cancer evolution and of sequencing experiments.

Publication Type: Academic Journal

Source(s): BMC Bioinformatics. 7/8/2022, Vol. 23 Issue 1, p1-19. 19p.

Abstract: Background: The combined effects of biological variability and measurement-related errors on cancer sequencing data remain largely unexplored. However, the spatio-temporal simulation of multi-cellular systems provides a powerful instrument to address t...

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Assessing Confidence in Root Placement on Phylogenies: An Empirical Study Using Nonreversible Models for Mammals.

Publication Type: Academic Journal

Source(s): Systematic Biology. Jul2022, Vol. 71 Issue 4, p959-972. 14p.

Abstract: Using time-reversible Markov models is a very common practice in phylogenetic analysis, because although we expect many of their assumptions to be violated by empirical data, they provide high computational efficiency. However, these models lack the ab...

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Brauer and partition diagram models for phylogenetic trees and forests.

Publication Type: Academic Journal

Source(s): Proceedings of the Royal Society A: Mathematical, Physical & Engineering Sciences. Jun2022, Vol. 478 Issue 2262, p1-25. 25p.

Abstract: We introduce a correspondence between phylogenetic trees and Brauer diagrams, inspired by links between binary trees and matchings described by Diaconis and Holmes (1998 Proc. Natl Acad. Sci. USA95, 14 600–14 602. (doi:10.1073/pnas.95.25.14600)). This ...

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