On 2013 Jun 26, Matthew Stephens commented:

This paper is a beautiful example of a simple idea leading to useful inference (and a type of inference that is generally really difficult). I have to admit I would never have tried this myself, anticipating that variation in mutation rate across the genome would have caused too many problems, but it seems that this is less of a concern than I would have expected.

On 2013 Jun 26, Matthew Stephens commented:

This paper is a beautiful example of a simple idea leading to useful inference (and a type of inference that is generally really difficult). I have to admit I would never have tried this myself, anticipating that variation in mutation rate across the genome would have caused too many problems, but it seems that this is less of a concern than I would have expected.