> For the complete documentation index, see [llms.txt](https://phyfum.gitbook.io/tutorial/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://phyfum.gitbook.io/tutorial/phyfum.md). # Phyfum Phyfum is a tool for inferring phylogenetic trees on methylation-based studies. We harness fluctuating CpG (fCpG) sites of methylation arrays to study the clonal evolution of samples. You can read more about fCpGs in the [original paper](https://www.nature.com/articles/s41587-021-01109-w). We have implemented a phylogenetic model within BEAST v.1.8.4 based on the original described in the above paper. We have also designed a snakemake-based pipeline, covering the IDAT preprocessing, fCpG calling, automatic XML generation and BEAST inference. Additionally, if both tumor and reference samples are available, CNVs are called to curate non-fluctuating CpGs. Before you start using the tool, we recommend you reading [The workflow](/tutorial/the-workflow.md) section to fully understand how Phyfum works. --- # Agent Instructions This documentation is published with GitBook. GitBook is the documentation platform designed so that both humans and AI agents can read, navigate, and reason over technical content effectively. Learn more at gitbook.com. ## Querying This Documentation If you need additional information that is not directly available in this page, you can query the documentation by asking a question. Perform an HTTP GET request on the following URL with the `ask` and `goal` query parameters: ``` GET https://phyfum.gitbook.io/tutorial/phyfum.md?ask=&goal= ``` `ask` is the immediate question: it should be specific, self-contained, and written in natural language. `goal` is what the user is ultimately trying to achieve, the reason they need the answer. Sharing it helps GitBook give you a better, more relevant answer. A goal is most helpful when it describes the outcome the user wants rather than restating the question. For example, with `ask=how do I create an API token`, a goal like `automate deployments from our CI pipeline` lets GitBook tailor the answer to that use case. The response will contain a direct answer to the question and relevant excerpts and sources from the documentation. Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.