njs

0th

Percentile

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

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

Keywords
models
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".

References

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

See Also

nj, bionj, triangMtds

Aliases
  • njs
  • bionjs
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
Documentation reproduced from package ape, version 3.2, License: GPL (>= 2)

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