TreeOfLife.jl

TreeOfLife.jl defines data types for cladograms and chronograms in phylogenetics and methods analyzing these trees.

In development.

Alternative packages include:

• Phylo.jl ("in beta", and its outdated prototype Phylogenetics.jl)
• PhyloTrees.jl
• TreeTools.jl
• Phylogenies.jl ("in development")

Examples

The followings are some simple examples illustrating the usage of this package. Please see the documentation for more details of TreeOfLife.jl.

julia> using TreeOfLife

julia> tree = fromnewick("(A:0.1,B:0.2,(C:0.3,D:0.4)E:0.5)F;")
ChronoTree(ChronoNode[ChronoNode("F", 0, 0, 2, 0.0, 0.0), ChronoNode("A", 1, 3, 0, 0.1, 0.1), ChronoNode("B", 1, 4, 0, 0.2, 0.2), ChronoNode("E", 1, 0, 5, 0.5, 0.5), ChronoNode("C", 4, 6, 0, 0.8, 0.3), ChronoNode("D", 4, 0, 0, 0.9, 0.4)])

julia> tonewick(tree)
"(A:0.1,B:0.2,(C:0.3,D:0.4)E:0.5)F;"

julia> tipnames = gettipnames(tree)
4-element Vector{String}:
 "A"
 "B"
 "C"
 "D"

julia> getmrca(tree, tipnames)
1

julia> getphylodiv(tree, tipnames)
1.5

julia> ismonophyl(tree, ["A", "B"])
false

julia> ismonophyl(tree, ["C", "D"])
true