PhISCS

PhISCS (Phylogeny Inference from Single-Cell Sequencing) is a software tool that infers tumor phylogenies from single-cell sequencing (SCS) data. It aims to reconstruct the evolutionary history and lineage relationships of cancer cells within a tumor.

Key features and functionalities of PhISCS include:

1. Utilizes SCS data: PhISCS takes advantage of the high-resolution information provided by single-cell sequencing technologies to capture the genetic heterogeneity within a tumor.

2. Probabilistic approach: The tool employs a probabilistic model to account for the noise and errors inherent in SCS data, such as allelic dropout and false-positive mutations.

3. Mutation tree inference: PhISCS infers the most likely mutation tree that represents the evolutionary relationships among the cancer cells. It identifies the order in which mutations occurred and the lineages that gave rise to different subclones within the tumor.

4. Subclone identification: By analyzing the mutation patterns across single cells, PhISCS can identify distinct subclones or subpopulations of cells that share common mutations and evolutionary histories.

5. Visualization: The tool provides visualization capabilities to represent the inferred tumor phylogeny, allowing researchers to explore the evolutionary landscape of the tumor.

6. Handling technical artifacts: PhISCS incorporates methods to handle technical artifacts commonly present in SCS data, such as doublets (two cells captured together) and sequencing errors.