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")`

- dataset
A phylogenetic data matrix of class

`phyDat`

, whose names correspond to the labels of any accompanying tree.- constraint
An object of class

`phyDat`

; returned trees will be perfectly compatible with each character in`constraint`

. See vignette for further examples.- weight
Numeric specifying degree to up-weight characters in

`constraint`

.- ratio
Settings of

`ambig`

and`ratio`

to be used when computing`Hamming()`

distances between sequences.- ambig
Settings of

`ambig`

and`ratio`

to be used when computing`Hamming()`

distances between sequences.

`ConstrainedNJ()`

returns a tree of class `phylo`

.

Other tree generation functions:
`GenerateTree`

,
`NJTree()`

,
`SingleTaxonTree()`

,
`TreeNumber`

```
dataset <- MatrixToPhyDat(matrix(
c(0, 1, 1, 1, 0, 1,
0, 1, 1, 0, 0, 1), ncol = 2,
dimnames = list(letters[1:6], NULL)))
constraint <- MatrixToPhyDat(
c(a = 0, b = 0, c = 0, d = 0, e = 1, f = 1))
plot(ConstrainedNJ(dataset, constraint))
```