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kdetrees (version 0.1.2)

Nonparametric method for identifying discordant trees

Description

Given a set of phylogenetic trees on a group of taxa (for example trees based on individual gene sequences), we present a method for identifying a subset of trees which are discordant with the other trees in the set. These discordant trees may arise from either biologically interesting phenomena (horizontal gene transfers, for example) or more mundane sequencing or annotation errors.

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Version

Install

install.packages('kdetrees')

Monthly Downloads

9

Version

0.1.2

License

GPL-2

Maintainer

Ruriko Yoshida

Last Published

February 9th, 2013

Functions in kdetrees (0.1.2)

plot.kdetrees

Plot the unnormalized density estimates for each tree.
kdetrees

Identify discordant trees in a sample
dist.diss

pairwise tree distances
kdetrees-package

kdetrees
normkern

Generalized Gaussian kernel
bw.nn

nearest-neighbor adaptive bandwidth selection
apicomplexa

Apicomplexa gene trees sample data set.
hist.kdetrees

Create a histogram of tree density estimates
dissmap

dissimilarity map tree vectorization
estimate

estimate densities from kernel matrix