ShainLab/Phylogenetic_tree: Phylogenetic tree

This release provides the first public version of Phylogenetic_tree, a software toolkit developed in the Shain Laboratory for constructing and visualizing phylogenetic trees from somatic mutation and clonal sequencing data.

Phylogenetic_tree implements methods to infer evolutionary relationships among samples or clones using variant call data, supporting downstream analysis of clonal dynamics, mutation accumulation, and lineage tracing. The toolkit includes utilities for tree construction, annotation, and export to common visualization formats.

This initial release corresponds to the version of the code used in internal analyses and publications involving evolutionary reconstruction of somatic mutations and clonal populations.

License: MIT License

Please cite the Zenodo DOI associated with this release when using this software in publications.

Changes in v1.0.0:

• Initial public release of Phylogenetic_tree
• Tools for constructing and visualizing phylogenetic trees from somatic variant data
• Documentation and example usage included