Tree Reconstruction from Incomplete Distances With NJ* or bio-NJ*
Reconstructs a phylogenetic tree from a distance matrix with possibly missing values.
njs(X, fs = 15) bionjs(X, fs = 15)
- a distance matrix.
- 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
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