Hello everyone,

I have previously worked with gene tree/species tree evolution tools but not tumor evolution so if it looks like a silly question, I beg your pardon.

I have variant calling data (using Mutect and VarScan) for whole-exome sequencing data. In the review paper, such as http://sysbio.oxfordjournals.org/content/64/1/e1, the authors say that, for instance, for PyClone, Phylosub and SciClone, the input data is single nucleotide variant (SNV). When I check, for instance, in test data in PyClone, it has a nicely formatted input file which is used to generate the output.

I am wondering if someone has worked with any pipeline for phylogenetic tree reconstruction using "any" of tumor evolution software? I would be grateful if you can share your experience (and, if possible, the steps).

Thanks in advance
Once you've clustered your data to identify subclonal populations (with the algorithms you list above), there are a few different tools that will attempt to construct evolutionary trees. The ones I'm aware of are below:

ClonEvol: https://github.com/hdng/clonevol

SubcloneSeeker: http://www.genomebiology.com/2014/15/8/443

Schism: http://karchinlab.org/apps/appSchism.html