njs {ape} | R Documentation |
Reconstructs a phylogenetic tree from a distance matrix with possibly missing values.
njs(X, fs = 15) bionjs(X, fs = 15)
X |
a distance matrix. |
fs |
argument s of the agglomerative criterion: it is coerced as an integer and must at least equal to one. |
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).
an object of class "phylo"
.
Andrei Popescu
Criscuolo, A., Gascuel, O. (2008) Fast NJ-like algorithms to deal with incomplete distance matrices. BMC Bioinformatics, 9, 166.
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