Kdetrees specifications

Information


Unique identifier OMICS_04172
Name Kdetrees
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 0.1.5
Stability Stable
Requirements
ggplot2, R(≥2.15.1), ape, distory
Maintained Yes

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Publication for Kdetrees

Kdetrees in publications

 (3)
PMCID: 5938378
PMID: 29765358
DOI: 10.3389/fmicb.2018.00771

[…] model. fasttree was compiled with double-precision enabled for maximum accuracy (see the manual for details). the resulting gene trees are screened to detect “outliers” with help of the r package kdetrees (v.0.1.5) (weyenberg et al., , ). it implements a non-parametric test based on the distribution of tree topologies and branch lengths expected under the multispecies coalescent, identifying […]

PMCID: 5793493
PMID: 29422694
DOI: 10.1093/biomet/asx047

[…] included as an out-group, scyliorhinus canicula, leucoraja erinacea and callorhinchus milii., analysis was performed ignoring pendant edge lengths. a total of 97 outlying trees were removed using kdetrees (), so that 1193 gene trees remained. the fréchet mean was computed using the bačák algorithm and its topology is shown in . the mean tree does not resolve whether coelacanth or lungfish […]

PMCID: 4868114
PMID: 26893301
DOI: 10.1093/molbev/msw038

[…] from the position of the primary misannotated species. fig. 8. , given the “outlier” nature of the loci identified in the small cluster, we also applied a specialized outlier detection package, kdetrees (). remarkably, with geodesic distances, it identified the exact same 37 loci as outliers (supplementary fig. s9, supplementary material online). this provides additional evidence […]


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Kdetrees institution(s)
Department of Statistics, University of Kentucky, Lexington, KY, USA; Robotics Institute, Carnegie Mellon University, Pittsburgh, PA, USA; Plant Pathology Department and Department of Veterinary Science, University of Kentucky, Lexington, KY, USA

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