mvr

0th

Percentile

Minimum Variance Reduction

Phylogenetic tree construction based on the minimum variance reduction.

Keywords
models
Usage
mvr(X, V)
mvrs(X, V, fs = 15)
Arguments
X
a distance matrix.
V
a variance matrix.
fs
agglomeration criterion parameter: it is coerced as an integer and must at least equal to one.
Details

The MVR method can be seen as a version of BIONJ which is not restricted to the Poison model of variance (Gascuel 2000).

Value

  • an object of class "phylo".

References

Criscuolo, A. and Gascuel, O. (2008). Fast NJ-like algorithms to deal with incomplete distance matrices. BMC Bioinformatics, 9.

Gascuel, O. (2000). Data model and classification by trees: the minimum variance reduction (MVR) method. Journal of Classification, 17, 67--99.

See Also

bionj, fastme, njs, SDM

Aliases
  • mvr
  • mvrs
Examples
data(woodmouse)
rt <- dist.dna(woodmouse, variance = TRUE)
v <- attr(rt, "variance")
tr <- mvr(rt, v)
plot(tr, "u")
Documentation reproduced from package ape, version 3.2, License: GPL (>= 2)

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