NeighborJoining

NeighborJoining

This package contains algorithms for neighbor joining

What is currently implemented?

• 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
• dynamic NeighborJoining dynamicNJ(): Clausen, P. T. L. C. Scaling neighbor joining to one million taxa with dynamic and heuristic neighbor joining. Bioinformatics 39, btac774 (2023).
  • exact (same tree as regNJ) but much faster on large inputs; multithreaded with julia -t auto

Installation

add NeighborJoining

Examples

# 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)

# or dynamic neighbor joining (exact, faster on large inputs, multithreaded)
njclusts = dynamicNJ(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)