I have methylation data (Illumina HumanMethylationEPIC) from multiple sites in a single tumor and I want to infer a phylogenetic tree for these samples. Using the R package
conumee, I can generate segmented copy number profiles for each sample. These segments each have a continuous copy number value that is relative to a normal tissue reference.
I am now looking for a way to get a phylogenetic tree out of this data. So far I plan on converting the continuous CN values into discrete ones (using ABSOLUTE algorithm, as suggested here) and then putting this data into TuMult algorithm (skipping TuMult's own segmentation step).
However, I'm wondering if there might be better methods, more tailored specifically to microarray methylation data. Do you know of any other algorithms or methods or literature out there suitably for this kind of problem?
Many thanks for your help :)