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Kdetrees specifications


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
ggplot2, R(≥2.15.1), ape, distory
Maintained Yes


No version available


Publication for Kdetrees

Kdetrees citations


GET_PHYLOMARKERS, a Software Package to Select Optimal Orthologous Clusters for Phylogenomics and Inferring Pan Genome Phylogenies, Used for a Critical Geno Taxonomic Revision of the Genus Stenotrophomonas

Front Microbiol
PMCID: 5938378
PMID: 29765358
DOI: 10.3389/fmicb.2018.00771

[…] el, and among-site rate variation was modeled fitting a gamma distribution with 20 rate categories (+G), as summarized in Table . Similar numbers of “outlier” trees (range 18:22) were detected by the kdetrees-test in the four search types (Table ). However, the distributions of SH-alrt support values are strikingly different for both search algorithms (Wilcoxon, p < 2.2e-16), revealing that gene-t […]


Principal component analysis and the locus of the Fréchet mean in the space of phylogenetic trees

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

[…] fish 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 is t […]


Clustering Genes of Common Evolutionary History

Mol Biol Evol
PMCID: 4868114
PMID: 26893301
DOI: 10.1093/molbev/msw038

[…] , aside 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 that these […]

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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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