Minimum Variance Reduction
Phylogenetic tree construction based on the minimum variance reduction.
mvr(X, V) mvrs(X, V, fs = 15)
- a distance matrix.
- a variance matrix.
- 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
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")