Constructs an approximation to a neighbour-joining tree, modified in order to be consistent with a constraint. Zero-length branches are collapsed at random.
ConstrainedNJ(dataset, constraint, weight = 1L, ratio = TRUE, ambig = "mean")
A phylogenetic data matrix of phangorn class
whose names correspond to the labels of any accompanying tree.
An object of class
phyDat; returned trees will be
perfectly compatible with each character in
for further examples.
Numeric specifying degree to up-weight characters in
ratio to be used when
Hamming() distances between sequences.
ConstrainedNJ() returns a tree of class