extract_mclade.jl: extracts maximum unrooted clades and the induced trees from mul-trees
Usage:
extract_mclade.jl <gene_trees> [<out>]
Input: mul-trees t[1] ... t[n] in a single file where labels are integers, in Newick format. To accomodate SimPhy, labels in the format of "x_y_z" are taken to be simply "x".
Output: the maximal elements (by proper subset) of the singly labeled clades generated by some unrooted subtree of some t
, along with
the trees that generated these clades.
julia extract_mclade.jl examples/g_trees.tre
This is written in Julia (unfortunately not Python, and AFAIK school clusters don't have Julia). Install Julia 1.5 and install the following packages
DocOpt, Multisets, Combinatorics, DataStructures
Or run the following in the Julia repl (running julia
in unix systems) to install the packages
using Pkg
for pkg = ["DocOpt", "Multisets", "Combinatorics", "DataStructures"]
Pkg.add(pkg)
end