TuELiP - an integer linear programming based method that given a set of potential tumor evolutionary histories, and weights for each one, finds a weighted consensus (or representative) history. Download (BitBucket)
CASet and DISC - distance measures designed to account for different sublconal inheritance patterns between tumor evolutionary trees. Download (BitBucket)
GraPhyC - an algorithm that given a set of potential tumor evolutionary histories, finds a consensus (or representative) history. Download (BitBucket)
H/T Alternating Fraction - a measurement of one potential signature of chromothripsis that can be computed using DNA sequencing data. Download (BitBucket)
AncesTree - an algorithm that infers the clonal evolution and tumor composition, including mixing fractions, of a tumor from multi-sample DNA sequence data. Software Page Download (GitHub) Google Group
THetA/THetA2 - an algorithm that estimates the tumor purity and clonal/sublconal copy number aberrations directly from high-throughput DNA sequencing data. The latest release is called THetA2 and includes a number of improvements over previous versions. Software Page Download (GitHub) Google Group
PREGO - an algorithm that reconstructs a cancer genome as a rearrangement of segments, or intervals, from the reference genome using paired-end sequencing data. Software Page
Other - the programs listed above and all other software from the Raphael research group can be found at the following link. Software Page