> ## Documentation Index
> Fetch the complete documentation index at: https://demo.agenticlabs.com/llms.txt
> Use this file to discover all available pages before exploring further.

# Overview

## High-level description

The `cassiopeia` directory contains a comprehensive suite of tools and modules for phylogenetic analysis, particularly focused on single-cell lineage tracing experiments. It provides functionality for data preprocessing, tree reconstruction, simulation, visualization, and various analytical tools for working with phylogenetic trees.

## What does it do?

The Cassiopeia package offers a wide range of functionalities:

1. Data Preprocessing: Converts raw sequencing data to formats suitable for phylogenetic analysis, including filtering, error correction, and allele calling.

2. Tree Reconstruction: Implements various algorithms for reconstructing phylogenetic trees from mutation data, including greedy, distance-based, spectral, and integer linear programming methods.

3. Simulation: Provides tools to generate synthetic phylogenetic trees and associated data, allowing researchers to test and validate analysis methods.

4. Visualization: Offers both local and cloud-based options for visualizing phylogenetic trees and associated data.

5. Analysis Tools: Includes utilities for parameter estimation, fitness calculation, evolutionary coupling analysis, and various tree metrics.

6. Tree Comparison: Implements methods for comparing phylogenetic trees, such as Robinson-Foulds distance and triplets correct accuracy.

These functionalities enable researchers to perform end-to-end analysis of single-cell lineage tracing data, from raw sequencing results to detailed phylogenetic insights.

## Entry points

The main entry points for the Cassiopeia package are:

1. `cassiopeia.preprocess`: For preprocessing raw sequencing data.
2. `cassiopeia.solver`: For reconstructing phylogenetic trees from processed data.
3. `cassiopeia.simulator`: For generating synthetic phylogenetic data.
4. `cassiopeia.plotting`: For visualizing phylogenetic trees and associated data.
5. `cassiopeia.tools`: For various analytical tools and utilities.
6. `cassiopeia.critique`: For comparing and analyzing phylogenetic trees.

The `__init__.py` file in the root directory serves as the main interface, importing and exposing key functionalities from these submodules.

## Key Files

1. `data/CassiopeiaTree.py`: Defines the core data structure for representing phylogenetic trees with associated mutation data.
2. `solver/CassiopeiaSolver.py`: Provides the base class for tree reconstruction algorithms.
3. `simulator/TreeSimulator.py`: Offers the base class for tree simulation models.
4. `plotting/local.py` and `plotting/itol_utilities.py`: Implement local and cloud-based tree visualization.
5. `tools/parameter_estimators.py`: Contains functions for estimating key parameters from tree data.
6. `critique/compare.py`: Implements tree comparison algorithms.

## Dependencies

Cassiopeia relies on several external libraries:

1. numpy and pandas: For data manipulation and numerical computations.
2. networkx: For graph operations and tree manipulations.
3. scipy: For various scientific computing tasks.
4. ete3: For phylogenetic tree manipulation and visualization.
5. matplotlib and plotly: For local plotting.
6. pysam: For handling sequencing data formats.
7. cvxpy and gurobipy: For optimization problems in some solvers.

## Configuration

Cassiopeia uses configuration files and function parameters for customization:

1. Preprocessing pipeline: Configured using an INI-format file specifying parameters for each preprocessing step.
2. Solvers: Customizable through parameters passed during initialization.
3. Simulators: Configurable via parameters set during object creation.
4. Visualization: Customizable through function parameters for both local and cloud-based plotting.

Users can adjust these configurations to adapt Cassiopeia to their specific experimental setups and analysis requirements.

In summary, Cassiopeia provides a comprehensive framework for analyzing single-cell lineage tracing data, offering tools for every step from raw data processing to advanced phylogenetic analysis and visualization.