mvr {ape} | R Documentation |
Phylogenetic tree construction based on the minimum variance reduction.
mvr(X, V) mvrs(X, V, fs = 15)
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. |
The MVR method can be seen as a version of BIONJ which is not restricted to the Poison model of variance (Gascuel 2000).
an object of class "phylo"
.
Andrei Popescu
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.
data(woodmouse) rt <- dist.dna(woodmouse, variance = TRUE) v <- attr(rt, "variance") tr <- mvr(rt, v) plot(tr, "u")