damicore-tree-builder
damicore-tree-builder builds a deterministic Neighbor Joining tree from a
distance matrix and its labels. It is the third stage of the DAMICORE pipeline;
most users install the aggregate damicore distribution, which runs all four
stages end to end. Install this package alone to build trees without the rest of
the pipeline.
pip install damicore-tree-builder
Python
from damicore_tree_builder import build_tree
result = build_tree("distance.npy", "labels.json", "run")
distance.npy and labels.json are produced by the sibling damicore-distance
distribution; the call writes tree.json plus Newick, and tree.json is the
input the sibling damicore-clusterizer distribution consumes. The path API
copies into a temporary memory map, reuses slots, evaluates Q pairwise without
materializing it, and preserves negative branches. neighbor_joining(matrix, labels) is available for small in-memory matrices.
Links
- Repository: https://github.com/Delbem-Research-and-Innovation/damicore
- Issues: https://github.com/Delbem-Research-and-Innovation/damicore/issues
- Documentation: https://github.com/Delbem-Research-and-Innovation/damicore/blob/main/docs/quickstart.md
Licensed under Apache-2.0.
1 maintainer
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