Not WES but WGS, you might apply phyloWGS.

You can find it from googling and you can find other similar tools.

Best

It's usually done from genome sequencing data and quite difficult to do clonal reconstruction from exome sequencing data. The authors of clonsHD helped me doing some analysis using exome sequencing data. It might be worth checking their code on GitHub.

http://www.cell.com/cell-reports/fulltext/S2211-1247%2814%2900373-8

https://github.com/andrej-fischer/cloneHD

Thanks for the answers. I am in fact studying a tumor precursor that is genetically simplistic and only has 3-5 point mutations. What program would be the best to elucidate the temporal order of these 3-5 mutations based on deep sequencing data (WES or target panel)? The mutant allele frequencies of these mutations within a given tumor are very different.