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