R: Minimum Variance Reduction

mvr {ape} | R Documentation

## Minimum Variance Reduction

### Description

Phylogenetic tree construction based on the minimum variance reduction.

### 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"`.

### Author(s)

Andrei Popescu niteloserpopescu@gmail.com

### 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`

### Examples

    data(woodmouse)
    rt <- dist.dna(woodmouse, variance = TRUE)
    v <- attr(rt, "variance")
    tr <- mvr(rt, v)
    plot(tr, "u")

[Package ape version 5.1 Index]