lineagetools

Lineagetools is an open-source software library designed to help researchers manage, analyze, and visualize lineage data. The project provides data models and utilities for representing lineage as trees or directed acyclic graphs, supporting applications in genetics, cell lineage tracing, and genealogical research.

Core features include modular data ingestion, graph operations, and basic lineage inference. It accepts common formats such as CSV and JSON and also supports lineage-oriented representations similar to parent-child records. The toolkit offers operations to add, prune, and merge branches, compute generation depth, and identify ancestral relationships. It also includes lightweight lineage inference routines to assemble plausible structures from partial records and integrates with broader graph-analysis ecosystems for advanced analytics.

Lineagetools is implemented in Python and designed to be both library and command-line friendly. Its architecture centers on a core lineage graph object, with extensible parsers and visualization backends. The library emphasizes interoperability, providing export and import options in JSON, YAML, GraphML, and DOT formats for Graphviz, as well as hooks to other tools such as NetworkX for specialized analysis.

Typical use cases include constructing lineage trees from experimental or genealogical data, tracing descendants or ancestors, and performing generation-level statistics. Example workflows involve building a graph from parent-child pairs, computing generation counts, and extracting sublineages for focused study.

The project is maintained by an open-source community and released under a permissive license. Documentation, tutorials, and tests accompany the codebase to facilitate adoption and contribution. Lineagetools relates to broader resources in phylogenetics, genealogy, and graph analysis. Related tools include ETE Toolkit, Bio.Phylo, and NetworkX.