BitPhylogeny - A probabilistic framework for reconstructing intra-tumor phylogenies
BitPhylogeny is a probabilistic framework to reconstruct intra-tumor evolutionary pathways. Using a full Bayesian approach, we jointly estimate the number and composition of clones in the sample as well as the most likely tree connecting them.
Presentations:
Download and Installation
You can download BitPhylogeny from https://bitbucket.org/ke_yuan/bitphylogeny
Requirements:
- Python: NumPy,SciPy scikit-learn: http://scikit-learn.org/stable/ rpy2: http://rpy.sourceforge.net/
- R: rPython, mcclust, e1071, igraph, gplots, riverplot.
Installation:
- Clone the BitPhylogeny repository git clone git@bitbucket.org:ke_yuan/bitphylogeny.git cd bitphylogeny
- Install the BitPhylogeny python package cd python sudo python setup.py install
- Install the R package cd ../R R CMD INSTALL bitphylogenyR_0.1.tar.gz
References:
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BitPhylogeny: A probabilistic framework for reconstructing intra-tumor phylogenies
K. Yuan*, T. Sakoparnig*, F. Markowetz^, N. Beerenwinkel^
Genome Biology, 2015, 16:36
PMID:25786108 | doi:10.1186/s13059-015-0592-6
