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