ape (version 5.8)

njs: 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)

Value

an object of class "phylo".

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.

Author

Andrei Popescu

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).

References

Criscuolo, A., Gascuel, O. (2008) Fast NJ-like algorithms to deal with incomplete distance matrices. BMC Bioinformatics, 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