cassiopeia/preprocess
: For preprocessing raw sequencing data.cassiopeia/solver
: For reconstructing phylogenetic trees from processed data.cassiopeia/simulator
: For generating synthetic phylogenetic data.cassiopeia/plotting
: For visualizing phylogenetic trees and associated data.cassiopeia/tools
: For various analytical tools and utilities.cassiopeia/critique
: For comparing and analyzing phylogenetic trees.cassiopeia/__init__.py
file serves as the main interface, importing and exposing key functionalities from these submodules.
cassiopeia/data/CassiopeiaTree.py
: Defines the core data structure for representing phylogenetic trees with associated mutation data.cassiopeia/solver/CassiopeiaSolver.py
: Provides the base class for tree reconstruction algorithms.cassiopeia/simulator/TreeSimulator.py
: Offers the base class for tree simulation models.cassiopeia/plotting/local.py
and cassiopeia/plotting/itol_utilities.py
: Implement local and cloud-based tree visualization.cassiopeia/tools/parameter_estimators.py
: Contains functions for estimating key parameters from tree data.cassiopeia/critique/compare.py
: Implements tree comparison algorithms.build.py
: Handles the building and compilation of Cython extensions for performance-critical components.README.md
: Provides an overview of the project, installation instructions, and links to documentation and tutorials.pyproject.toml
: Defines project metadata, dependencies, and build settings..readthedocs.yml
: Configures the documentation build process on Read the Docs.codecov.yml
: Sets coverage requirements for the project.test
directory, ensuring the reliability and accuracy of the framework across its various modules and functionalities.
In summary, Cassiopeia provides a robust and flexible framework for analyzing single-cell lineage tracing data, offering tools for every step from raw data processing to advanced phylogenetic analysis and visualization.