SPRUCE is an algorithm that infers a multi-state perfect phylogeny describing the evolutionary history of the somatic mutations (SNVs and CNVs) of a tumor given multi-sample bulk sequencing data. Specifically, the input to SPRUCE are variant allele frequencies and copy-number mixing proportions for each SNV in each sample.
You can download the latest version of SPRUCE from the SPRUCE GitHub project.
For support, please see the SPRUCE Google Group.
SPRUCE is described in the following publications:
M. El-Kebir, G. Satas, L. Oesper, and B.J. Raphael. Inferring the Mutational History of a Tumor using Multi-State Perfect Phylogeny Mixtures Cell Systems, (2016) 3(1):43-53.
M. El-Kebir, G. Satas, L. Oesper, and B.J. Raphael. Multi-State Perfect Phylogeny Mixture Deconvolution and Applications to Cancer Sequencing RECOMB 2016.