This repository contains software and analysis code used for the publication The Evolutionary history of 2,658 cancers, Nature

The repository is organised into multiple git submodules pointing to individual repositories and the version of code used for the analysis. It is recommended to check out the most recent version of each software tool for future analyses.

At current the repository contains the following modules.

• MutationTimeR An R package to time copy number gains and point mutations as shown in Extended Data Figure 2.

• EBI This repository contains analysis code for Figures 1b,e-h, 2, 4, 5 & Extended Data Figures 3, 6, 8 and 9 and output underlying Extended Data Figure 2. The output of the code is an rmarkdown html report, hosted at https://gerstung-lab.github.io/PCAWG-11.

• PhylogicNDT A Python package to, among others, perform evolutionary league model analysis related to Figure 3 & Extended Data Figure 2,4 and 5.

• Crick A collection of R scripts for timing and signature analysis, related to Figure 1c,d, 4c,d & Extended Data Figure 2 and 7.

Please refer to the original repositories (links provided above) for the exact requirements and run times.

Please check out this repository using

git clone --recurse-submodules https://github.com/PCAWG-11/Evolution.git

which automatically retrieves all submodules.