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.

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 section to fully understand how Phyfum works.