Question on output format

[seidels]

Hi there,
thank your developing MERLIN!

I have a few questions on the output format. In the example data, the _Umatrix.csv and the related _Amatrix.csv provide cell by mutation matrices. Why are they not cell by clone matrices (as depicted in Fig 2. of the manuscript)? How can I get a cell by clone output from MERLIN? Or am I missing something obvious?

[teng-gao]

Similar question - I guess that the unique sets of mutations already define clones. But getting a clone tree like the figures in the paper is not straightforward to me