SCITE

SCITE is a software tool for the deduction of tumors' evolutionary history from single-cell mutation profiles that can be incomplete. The SCITE algorithm uses Markov chain Monte Carlo (MCMC) sampling and maximum-likelihood (ML) methods. infSCITE extends SCITE by allowing sampling from two cells and testing of the validity of a single-cell mutation matrix.

Topic

Oncology;Machine learning;Phylogenetics

Detail

Operation: Phylogenetic tree analysis
Software interface: Command-line user interface
Language: C++
License: GNU General Public License v3
Cost: Free
Version name: -
Credit: RTD Grant (http:--www.systemsx.ch-), ERC Synergy Grant (http:--erc.europa.eu-).
Input: Mutation matrix
Output: ML/MAP trees
Contact: Niko Beerenwinkel niko.beerenwinkel@bsse.ethz.ch
Collection: -
Maturity: -

Publications

Tree inference for single-cell data.
Jahn K, Kuipers J, Beerenwinkel N. Tree inference for single-cell data. Genome Biol. 2016 May 5;17:86. doi: 10.1186/s13059-016-0936-x. PMID: 27149953; PMCID: PMC4858868.
https://doi.org/10.1186/s13059-016-0936-x
PMID: 27149953
PMC: PMC4858868

Download and documentation

Source: https://github.com/cbg-ethz/SCITE
Documentation: https://github.com/cbg-ethz/SCITE/blob/master/README.md
Home page: https://github.com/cbg-ethz/SCITE
Links: https://github.com/cbg-ethz/infSCITE
Links: https://gitlab.com/jahnka/SCITE

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