4 \title{Tree Reconstruction from Incomplete Distances With NJ* or bio-NJ*}
6 Reconstructs a phylogenetic tree from a distance matrix with possibly
14 \item{X}{a distance matrix.}
15 \item{fs}{argument \emph{s} of the agglomerative criterion: it is
16 coerced as an integer and must at least equal to one.}
19 Missing values represented by either \code{NA} or any negative number.
21 Basically, the Q* criterion is applied to all the pairs of leaves, and
22 the \emph{s} highest scoring ones are chosen for further analysis by
23 the agglomeration criteria that better handle missing distances (see
24 references for details).
27 an object of class \code{"phylo"}.
30 \url{http://www.biomedcentral.com/1471-2105/9/166}
32 \author{Andrei Popescu \email{niteloserpopescu@gmail.com}}
34 \code{\link{nj}}, \code{\link{bionj}}, \code{\link{triangMtds}}
38 d <- dist.dna(woodmouse)
40 dm[sample(length(dm), size = 3)] <- NA
41 dist.topo(njs(dm), nj(d)) # often 0
42 dm[sample(length(dm), size = 10)] <- NA
43 dist.topo(njs(dm), nj(d)) # sometimes 0