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AncesTree: An algorithm for clonal tree reconstruction from multi-sample cancer sequencing data
cna-processing: Script for taking the output of the GISTIC2.0 module and converting the data for use with MAGI, HotNet2, and CoMEt.
CNT-ILP: Integer Linear Program for the Copy-Number Tree Problem
CNT-MD: Software for inferring the copy-number profiles of tumor clones and their evolution from fractional copy numbers obtained from multi-sample bulk sequencing data.
comet: CoMEt: A Statistical Approach to Identify Combinations of Mutually Exclusive Alterations in Cancer
gd3: Javascript library for visualizing genomics data with D3.
heinz: Single species module discovery
hierarchical-hotnet: Hierarchical HotNet is an algorithm for finding hierarchies of active subnetworks.
hotnet: HotNet is an algorithm for finding significantly altered subnetworks in a large gene interaction network.
hotnet2: HotNet2 is an algorithm for finding significantly altered subnetworks in a large gene interaction network
machina: Framework for Metastatic And Clonal History INtegrative Analysis
magi: A web application from the Raphael Lab for mutation annotation and genome interpretation.
magi-annotations: null
magi-images: Docker images for deploying the MAGI web app
magi-stat-server: A JSON-based statistics server in Tornado for supplying enrichments to MAGI
multibreak-sv: MultiBreak-SV identifies structural variants from next-generation paired end data, third-generation long read data, or data from a combination of sequencing platforms.
multi-dendrix: null
NAIBR: Novel Adjacency Identification with Barcoded Reads
PASTRI: null
Perfect-Phylogeny-Constructor-and-Visualizer: null
RAIG: null
raphael-group.github.io: Raphael group website.
snv-processing: A script for converting MAF files for use with MAGI, CoMEt, and HotNet2.
spruce: SPRUCE: Somatic Phylogeny Reconstruction using Combinatorial Enumeration
TADtree: null
THetA: Tumor Heterogeneity Analysis (THetA) is an algorithm that estimates the tumor purity and clonal/subclonal copy number aberrations directly from high-throughput DNA sequencing data. Please note that the latest release is now called THetA2.
wext: A Weighted Exact Test for Mutually Exclusive Mutations in Cancer

This work is supported by the National Institutes of Health's National Center for Advancing Translational Sciences, Grant Number U24TR002306. This work is solely the responsibility of the creators and does not necessarily represent the official views of the National Institutes of Health.