Multi region tumor Phylogenic tree

Question

[Nickier]

Hi, I want to create a sample Phylogenic tree based on the somatic mutation data, multi-regions from a same tumor , as shown in the figure. Now that I have obtained the binomial matrix of mutations, I don’t know what to do next. I also want to know how to add genes on the trunk and branch.

paper: Tracking the Genomic Evolution of Esophageal Adenocarcinoma through Neoadjuvant Chemotherapy

[Mark]

The paper says phangorn package was used to construct the phylogenies:

https://cran.r-project.org/web/packages/phangorn/index.html

It was probably used to also visualise the trees because the examples look very similar.

[Nickier]

Thanks Mark, I have got the results with phangorn.