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FastMulRFS Example

Step 0: Clone this repository.

git clone https://github.com/ekmolloy/fastmulrfs.git
cd example

Step 1: Preprocess gene family trees. This transforms each MUL-tree into singly-labeled (and potentially unresolved) tree. Importantly, the optimal solution to the MulRF supertree optimization problem for the MUL-trees is the optimal solution to the RF supertree optimization problem for the preprocessed MUL-trees (Theorem 2). NOTE: If you haven't already, first install TreeSwift.

python ../python-tools/preprocess_multrees_v3.py \
    -i g_trees-mult.trees \
    -o g_trees-mult-for-fastrfs.trees \
    --verbose

Step 2: Run FastRFS, a heuristic for estimating a RF supertree, on the preprocessed gene family trees. NOTE: If you haven't already, first install FastRFS, as described here.

../external/FastRFS/build/FastRFS \
        -i g_trees-mult-for-fastrfs.trees \
        -o fastmulrfs.tree &> fastmulrfs.log

Also see this bash script.