CLONES

CLONES is a C++ Library fOr Neoplastic Evolution Simulations.

CLONES simulates cancer genomic evolution. It supports:

• cell strand competition and spacial simulations
• epigenetic switches
• copy-number variations
• SBS and indel signature support
• sequencing simulation

CLONES also provides 6 CLI tools:

• species_sim performs cell spacial simulation by using species evolutionary information. It supports epigenetic switching.
• build_context_index creates an index for the mutational contexts (i.e., consecutive triplets of nucleotides) in a genome. This index is used to place passenger SNVs according to SBS signatures. In normal conditions, the context index for a genome must be created once for all and the resulting file can be used many times.
• build_repetition_index creates an index for the repeated sequences in a genome. This index is used to place indels according to ID signatures. As for the build_context_index, the repeated sequences index for a genome must be created once for all and the resulting file can be used many times.
• tissue_sampler samples the results of species_sim.
• descendants_builder builds the descendants forest from the species simulation.
• mutations_sim builds the phylogenetic forest for the sampled cells, and places mutations (only SNVs and CNAs are supported at the moment) on the tree. It can:
  • produce simulated reads and generate the corresponding SAM file for them;
  • collect SNVs, indels, and CNAs statistical data and save them in CSV files.

Required Packages

• CMake
• a C++20 compiler

CLI Tools Required Packages

• Boost::program_options
• nlohmann/json library

Optional Packages

• Boost::unit_test_framework (enabling C++ code testing)
• SDL_ttf and SDL_image libraries (enabling simulation plotting)
• Boost::Python (enabling incomplete Python bindings)

Setup

GNU/Linux and macOS

Once the required packages have been installed, use the following commands in a shell

git clone https://github.com/albertocasagrande/CLONES.git
cd CLONES
cmake .
make -j

Wrapper

• ProCESS is an R wrapper for CLONES.

License

Copyright (c) 2023-2026 Alberto Casagrande <alberto.casagrande@uniud.it>

MIT License

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.