'nancdist'<-
function(tree, taxaname)
{
ntaxa<-length(taxaname)
nodematrix<-read.tree.nodes(tree,taxaname)$nodes
if(is.rootedtree(nodematrix)) nodematrix<-unroottree(nodematrix)
dist<-matrix(0, ntaxa,ntaxa)
for(i in 1:(ntaxa-1))
for(j in (i+1):ntaxa)
{
anc1<-ancestor(i,nodematrix)
anc2<-ancestor(j,nodematrix)
n<-sum(which(t(matrix(rep(anc1,length(anc2)),ncol=length(anc2)))-anc2==0, arr.ind=TRUE)[1,])-3
if(n==-1) n<-0
dist[i,j]<-n
}
dist<-dist+t(dist)
z<-list(dist=as.matrix, taxaname=as.vector)
z$dist<-dist
z$taxaname<-taxaname
z
}
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