This package contains algorithms for neighbor joining
- regular Neighborjoining
regNJ(): Saitou, N. & Nei, M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Molecular Biology and Evolution 4, 406-425 (1987). - fast NeighborJoining
fastNJ(): Li, J. F. A fast neighbor joining method. Genet Mol Res 14, 8733–8743 (2015).- uses heuristics, will not always find the additive tree
add NeighborJoining
# make distance matrix
d = rand(10, 10)^2
for i in 1:size(d,1) d[i,i]=0 end;
# regular neighbor joining
njclusts = regNJ(d)
# or fast neighbor joining
njclusts = fastNJ(d)
# convert to newicktree string for export to other packages
nwstring = newickstring(njclusts)
# adding labels to the leaves
labels = ["leaf $i" for i in 1:10]
nwstring = newickstring(njclusts, labels)
# adding labels to the internal nodes
nwstring = newickstring(njclusts, labels; labelinternalnodes=true)