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 build directory:
| EXECUTABLE | DESCRIPTION |
|---|---|
cliques |
Enumerates cliques of the compatibility graph (given a size and a filter) |
enumerate |
Enumerates perfect phylogeny trees |
merge |
Merges multiple solution files into one |
rank |
Sorts solution trees by the fraction of common edges (solution with rank 0 is the most representative tree) |
visualize |
Visualizes one solution or the entire solution space |
For example usage see result/run_A22.sh and corresponding instructions.
For a description of the input file format see data/README.md.
For instructions on how to visualize the set of enumerated trees see src/visualization/README.md.