I think it would be really useful to have a list of packages / tools that allow to estimate tumor heterogeneity (spatial and temporal) and clonal analysis.

Some examples:

• TITAN : http://www.ncbi.nlm.nih.gov/pubmed/?term=25060187
• MEDICC : http://www.ncbi.nlm.nih.gov/pubmed/24743184
• THetA : http://www.ncbi.nlm.nih.gov/pubmed/23895164
• SciClone : http://www.ncbi.nlm.nih.gov/pubmed/25102416
• rec-BTP : http://www.ncbi.nlm.nih.gov/pubmed/24932008
• EXPANDS : http://www.ncbi.nlm.nih.gov/pubmed/24177718
• PhyloSub : http://www.ncbi.nlm.nih.gov/pubmed/24484323
• TuMult : http://www.ncbi.nlm.nih.gov/pubmed/20649963

Other suggestions?