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inference of phylogenetic trees

Bayesian inference of ancestral dates on bacterial phylogenetic trees

Bayesian inference of ancestral dates on bacterial phylogenetic trees

... for inference as in BEAST, but consider that phylogenetic relationships have been assessed in a previous step as in the optimization and maximum likelihood methods described ...Bayesian inference in ...

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Relating Phylogenetic Trees to Transmission Trees of Infectious Disease Outbreaks

Relating Phylogenetic Trees to Transmission Trees of Infectious Disease Outbreaks

... Optimal inference of transmission events calls for the combination of genetic data and epidemiological data into one joint ...the phylogenetic tree, which describes the ancestral relationships between ...

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Fast phylogenetic inference from typing data

Fast phylogenetic inference from typing data

... The proposed approach is particularly useful when one is interested in local phylogenies, i.e., local patterns of evolution, such as searching for similar sequences or pro- files in large typing databases, as in our ...

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Taxon ordering in phylogenetic trees by means of evolutionary algorithms

Taxon ordering in phylogenetic trees by means of evolutionary algorithms

... As starting tree for the algorithm, an original tree obtained by any available software for phylogenetic inference with any method (neighbor joining, maximum likelihood, maximum parsimony, Bayesian ...

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Bayesian Inference of the Evolution of a Phenotype Distribution on a Phylogenetic Tree

Bayesian Inference of the Evolution of a Phenotype Distribution on a Phylogenetic Tree

... the phylogenetic tree (Bhattacharya et ...virus phylogenetic tree or whether there are clades where the distributions are distinct from each ...10 phylogenetic trees from this data set and the ...

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Distance based Phylogenetic Trees with Bootstrapping

Distance based Phylogenetic Trees with Bootstrapping

... a phylogenetic tree, and this model has greatly facilitated the discussion and testing of hypotheses ...of phylogenetic trees is done by various ...reconstructing phylogenetic trees are ...

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Network dynamics of eukaryotic LTR retroelements beyond phylogenetic trees

Network dynamics of eukaryotic LTR retroelements beyond phylogenetic trees

... yses. In particular, we have inferred the evolutionary his- tory of the five groups addressed in the previous study. The phylogenetic inference is an important component of the manuscript. While the ...

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OrthoFinder: phylogenetic orthology inference for comparative genomics

OrthoFinder: phylogenetic orthology inference for comparative genomics

... orthogroup inference [10] and for gene tree inference of these orthogroups using DendroBLAST ...tree inference and sequence search to accommodate user ...gene trees do not need to be inferred ...

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HLA Footprints on Human Immunodeficiency Virus Type 1 Are Associated with Interclade Polymorphisms and Intraclade Phylogenetic Clustering

HLA Footprints on Human Immunodeficiency Virus Type 1 Are Associated with Interclade Polymorphisms and Intraclade Phylogenetic Clustering

... more phylogenetic clustering than that seen among the true sequences as a consequence of complete conservation of the mutations applied in the simulation com- pared to variations in the true sequences (number of ...

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Efficient Logical Inference for Semantic Processing

Efficient Logical Inference for Semantic Processing

... logical inference help RTE? Logical inference is shown to be useful for RTE, as Tian et ...logical inference only fills very limited short gaps from T to ...

5

The application of chordal graphs to inferring phylogenetic trees of languages

The application of chordal graphs to inferring phylogenetic trees of languages

... a phylogenetic tree and character data, determining the minimum number of edges one must add to produce a per- fect phylogeny network is NP-Hard (Day et ...

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Student construction of phylogenetic trees in an introductory biology course

Student construction of phylogenetic trees in an introductory biology course

... second phylogenetic tree construction exercise (Additional file 1: Figures S1–S2) was placed on the indi- vidual section of the comprehensive final ...third phylogenetic tree construction exercise ...

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Evolution of the streptomycin and viomycin biosynthetic clusters and resistance genes

Evolution of the streptomycin and viomycin biosynthetic clusters and resistance genes

... Obtaining gene sequences from organisms grown in pure culture is more straightforward than from environmental samples and ensures that all the genes amplified and sequenced from a sample originated from the same ...

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Found in Translation: Reconstructing Phylogenetic Language Trees from Translations

Found in Translation: Reconstructing Phylogenetic Language Trees from Translations

... reconstruct phylogenetic trees, with varying degrees of success (Nagata and Whittaker, 2013; Berzak et ...construct phylogenetic trees from ...

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treeman: an R package for efficient and intuitive manipulation of phylogenetic trees

treeman: an R package for efficient and intuitive manipulation of phylogenetic trees

... Background: Phylogenetic trees are hierarchical structures used for representing the inter-relationships between biological ...of phylogenetic trees—in terms of adding or removing tips—is ...

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Enumerating all maximal frequent subtrees in collections of phylogenetic trees

Enumerating all maximal frequent subtrees in collections of phylogenetic trees

... in canonical form. This step classifies T join as one of the four join types. If a particular join is supported by all the input trees (i.e. f = 1), the corresponding joined tree is an AST. A natural way to ...

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Heuristic assignment of CPDs for probabilistic inference in junction trees

Heuristic assignment of CPDs for probabilistic inference in junction trees

... Bayesian network, the architecture of the junction tree based algorithms for exact.. inference on BN's is briefly explained.[r] ...

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The Evolution of Sexually Selected Traits in Dance Flies.

The Evolution of Sexually Selected Traits in Dance Flies.

... similar in appearance. Both species typically prey on many families of Diptera including smaller empidid species and males of both species are usually found around trees with abundant sources of swarming prey. In ...

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EVOLUTIONARY CHANGE OF RESTRICTION CLEAVAGE SITES AND PHYLOGENETIC INFERENCE

EVOLUTIONARY CHANGE OF RESTRICTION CLEAVAGE SITES AND PHYLOGENETIC INFERENCE

... veloped for the probability of having a particular pattern of site changes among evolutionary lineages, such as parallel gains or losses of sites, and for inferring th[r] ...

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Limiting behaviour of Fréchet means in the space of phylogenetic trees

Limiting behaviour of Fréchet means in the space of phylogenetic trees

... as trees get further from T ∗ ...for trees in the orthant of T ∗ . For trees outside of this orthant, multiple trees can be mapped to the same Euclidean point, including two trees with ...

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