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maffe
maffe is an exact and heuristic solver for maximum agreement forest for two or more rooted bifurcating phylogenetic trees.
It won the first place in all three tracks (Exact, Heuristic, Lower Bound) of the PACE challenge 2026.
Acknowledgements The implementation was assisted by OpenAI’s Codex with GPT 5.4 and GPT 5.5. We extensively tested the solver with fuzzing and STRIDE instances and take responsibility for its correctness.
Python Library
python -m pip install maffe
Usage example:
import maffe
trees = ["((a,b),(c,d));", "((a,c),(b,d));"]
partition = maffe.solve(trees) # solve_unrooted for unrooted trees
print(partition) # [['a', 'b'], ['c'], ['d']]
forest = maffe.restrict_solution(trees, partition)
print(forest) # ['(a,b);', 'c;', 'd;']
distance = maffe.rspr_dist(*trees)
print(distance) # 2
Build From Source
Dependencies
- C++23 compiler
- Meson >= 1.3
- Ninja
- CMake
- Git
- pkg-config
- patch
The solver depends on SCIP Optimization Suite 10.0.2 and HiGHS 1.15.1. The competition build also uses ConicBundle for the heuristic binary. The Meson build script will automatically download and build all required solver dependencies. We optionally support Gurobi as (I)LP backend and expose Python bindings.
Build
On Debian/Ubuntu:
sudo apt-get update
sudo apt-get install -y build-essential meson ninja-build cmake git pkg-config patch
Configure and build:
meson setup build --buildtype=release
meson compile -C build
Run the solver with
./build/maffe < instance.trees
where instances.trees contains a list of bifurcating phylogenetic trees.
Competition Build
To build the competition binaries, which were submitted to optil.io and to the PACE Challenge 2026, use the Docker-based build script:
./scripts/build_competition.sh
This writes static binaries maffe-exact, maffe-heuristic, and maffe-lowerbound to dist-competition/.
However, for non-competition use, we recommend the default build.
1 maintainer
Metadata
1 maintainer
Release files for maffe 0.1.2
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Total release size: 141.9 MB
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| Download URL | maffe-0.1.2-cp311-cp311-manylinux_2_26_aarch64.manylinux_2_28_aarch64.whl |
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| Tags | CPython 3.11 Linux glibc 2.26+ ARM64 Linux glibc 2.28+ ARM64 |
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| Size | 5.6 MB |
| Tags | CPython 3.11 macOS 14.0+ ARM64 |
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