SPRUCE (Somatic Phylogeny Reconstruction using Combinatorial Enumeration) is an algorithm for inferring the clonal evolution of single-nucleotide and copy-number variants given multi-sample bulk tumor sequencing data.
For support using SPRUCE, please visit the SPRUCE Google Group.
SPRUCE is written C++. In addition to a recent C++ compiler (that supports C++11), it has the following dependencies:
Graphviz is required to visualize the resulting DOT files, but is not required for compilation.
To compile SPRUCE, execute the following commands from the root of the repository:
mkdir build cd build cmake .. make
In case CMake fails to detect LEMON, run the following command with adjusted paths:
cmake -DLIBLEMON_ROOT=~/lemon ..
The compilation results in the following files in the
||Enumerates cliques of the compatibility graph (given a size and a filter)|
||Enumerates perfect phylogeny trees|
||Merges multiple solution files into one|
||Sorts solution trees by the fraction of common edges (solution with rank 0 is the most representative tree)|
||Visualizes one solution or the entire solution space|
For instructions on how to visualize the set of enumerated trees see