phylogenetic inference
An Automated Framework for Fast Cognate Detection and Bayesian Phylogenetic Inference in Computational Historical Linguistics
... for phylogenetic infer- ...the phylogenetic inference task, since these datasets contain a large number of largely unre- solved dialect varieties for which no expert classi- fications are available ...
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Phylogenetic inference from homologous sequence data: minimum topological assumption, strict mutational compatibility consensus tree as the ultimate solution
... that the apparent homoplasy on the tree is minimal, and b) recognition of incompatible characters and their exclu- sion from the phylogenetic analysis [7]. Both approaches regard homoplasy as disturbing, adverse ...
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Continuous Space Representations of Linguistic Typology and their Application to Phylogenetic Inference
... Figure 2 shows the case of the Austroasiatic lan- guages. In the original, categorical representations, the mixtures of two languages form a deep valley (i.e., typologically unnatural intermediate states). By contrast, ...
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Current Methods for Automated Filtering of Multiple Sequence Alignments Frequently Worsen Single-Gene Phylogenetic Inference
... Abstract.—Phylogenetic inference is generally performed on the basis of multiple sequence alignments ...introduced phylogenetic tests of alignment accuracy on a large number of gene families and ...
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Trial by phylogenetics - Evaluating the Multi-Species Coalescent for phylogenetic inference on taxa with high levels of paralogy (Gonyaulacales, Dinophyceae)
... Figure 1. Maximum likelihood phylogenetic inference of ribosomal DNA genes. Concatenation of small subunit rDNA and D1-D3 region large subunit rDNA. Accession numbers for concatenated genes in Table S3. ...
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Fast phylogenetic inference from typing data
... Background: Microbial typing methods are commonly used to study the relatedness of bacterial strains. Sequence‑ based typing methods are a gold standard for epidemiological surveillance due to the inherent portability of ...
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Sporogony of four Haemoproteus species (Haemosporida: Haemoproteidae), with report of in vitro ookinetes of Haemoproteus hirundinis: phylogenetic inference indicates patterns of haemosporidian parasite ookinete development
... Background: Haemoproteus (Parahaemoproteus) species (Haemoproteidae) are widespread blood parasites that can cause disease in birds, but information about their vector species, sporogonic development and transmission ...
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Use of Endogenous Retroviral Sequences (ERVs) and structural markers for retroviral phylogenetic inference and taxonomy
... in phylogenetic inference and retroviral classification discussed here are: nucleotide bias, number of zinc fingers, translational strategy, C-terminal Pro and Pol motifs, presence of dUTPase and accessory ...
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Phylogenetic inference of calyptrates, with the first mitogenomes for Gasterophilinae (Diptera: Oestridae) and Paramacronychiinae (Diptera: Sarcophagidae)
... We are grateful to Drs. Jie Liu (Institute of Zo- ology, Chinese Academy of Sciences) and Eliana Buenaventura (Natural History Museum of Denmark, University of Copenhagen), Prof. Aibing Zhang and Miss Jie Qin (Capital ...
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Reconciling taxonomy and phylogenetic inference: formalism and algorithms for describing discord and inferring taxonomic roots
... The original algorithm described in Theorem 1 and the branch and bound algorithm in Algorithm 1 have been implemented in the rppr binary of the pplacer suite of pro- grams (http://matsen.fhcrc.org/pplacer). The code is ...
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Analysis of kinetoplast cytochrome b gene of 16 Leishmania isolates from different foci of China: different species of Leishmania in China and their phylogenetic inference
... applied phylogenetic techniques: heuristic searches using maximum parsimony (MP) analyses performed with the program PAUP* program and Bayesian inference (BI) using the MrBayes ...
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From alignment of etymological data to phylogenetic inference via population genetics
... statistical inference about language evolution under such models is complicated by the practi- cally intractable form of likelihoods for even a moderate set of ...lar phylogenetic model and for learning the ...
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A MULTI-GENE MOLECULAR SYSTEMATIC STUDY OF THE KICKXELLOMYCOTINA, INCLUDING THE EXAMINATION OF TWO NEW GENES (MCM7 AND TSR1) FOR PHYLOGENETIC INFERENCE
... Although Aguileta et al. (2008) demonstrated the utility and power of these two genes for phylogenetic analysis, neither primer sequences nor PCR protocols were provided. Schmitt et al. (2009) aligned amino acid ...
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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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Robust Entity Clustering via Phylogenetic Inference
... associated inference techniques, for the problem of cross-document coreference resolu- ...writers. Inference under such models could also play a role in tracking evolving memes and social influence, not ...
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Protein structure, distribution of homoplasy and phylogenetic inference
... A close look at the genetic code structure shows an asymmetry of nucleotide substitutions when there is a change of residue hydrophobicity and volume and current molecular model of evolu[r] ...
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Algebraic Geometry of Phylogenetic Models.
... The goal of phylogenetic inference is to find a tree that captures the evolutionary re- lationships between species. However, as referenced in Section 1.1, various biological phenomena confound this effort. ...
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The importance of phylogenetic model assessment for macroevolutionary inference
... using phylogenetic timescale estimates to study ...While phylogenetic estimates can provide some insight about macroevolution, it is becoming increasingly apparent that dispersal can be a primary driver of ...
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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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Refuting phylogenetic relationships
... The sequences of 34 genes identified as core genes in [12] were retrieved using the program "retrieve sequences" in all analyses of the Neurogadgets website [38] (option "Reciprocal best match in other ...
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