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.

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 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


[Package ape version 3.0 Index]