Cassiopeia: Simulated Single-Cell Phylogenies for Benchmarking Lineage Tracing

Synthetic benchmarking data includes simulated phylogenies of size 400 and 1000 cells. These phylogenies were generated with varying characters, states, experimental durations, mutation rates, dropout rates, and state distributions for the study 'Inference of single-cell phylogenies from lineage tracing data with Cassiopeia'. The dataset was created by Matthew G. Jones at UC Berkeley and published in Genome Biology.

Use Cases

• Benchmarking phylogenetic inference algorithms based on simulated phylogenies with varying parameters.
• Stress testing computational methods for lineage tracing based on simulated mutation and dropout rates.
• Analyzing the impact of experimental duration and state distribution on phylogenetic reconstruction accuracy.

Strengths

• Includes phylogenies of two specific sizes: 400 and 1000 cells.
• Simulations cover multiple parameters: characters, states, mutation rates, and dropout rates.
• Data is provided as pickled Python Networkx objects for convenient programmatic access.

Limitations

• Column-level documentation is absent; field semantics must be inferred after download.
• Row count is unknown, which may limit suitability assessment.
• Last update date is unknown; freshness unverified.

Provenance

Source

University of California, Berkeley

Collection Method

Synthetic data generation via simulation as described in the associated manuscript.