R: Tree Reconstruction from Incomplete Distances With NJ* or...

njs {ape} | R Documentation

## Tree Reconstruction from Incomplete Distances With NJ* or bio-NJ*

### Description

Reconstructs a phylogenetic tree from a distance matrix with possibly missing values.

### Usage

    njs(X, fs = 15)
    bionjs(X, fs = 15)

### Arguments

`X` | a distance matrix.
`fs` | argument s of the agglomerative criterion: it is coerced as an integer and must at least equal to one.

### Details

Missing values represented by either `NA` or any negative number.

Basically, the Q* criterion is applied to all the pairs of leaves, and the s highest scoring ones are chosen for further analysis by the agglomeration criteria that better handle missing distances (see references for details).

### Value

an object of class `"phylo"`.

### Author(s)

Andrei Popescu niteloserpopescu@gmail.com

### References

http://www.biomedcentral.com/1471-2105/9/166

### See Also

`nj`, `bionj`, `triangMtds`

### Examples

    data(woodmouse)
    d <- dist.dna(woodmouse)
    dm <- d
    dm[sample(length(dm), size = 3)] <- NA
    dist.topo(njs(dm), nj(d)) # often 0
    dm[sample(length(dm), size = 10)] <- NA
    dist.topo(njs(dm), nj(d)) # sometimes 0

[Package ape version 5.4 Index]