CoNe computes the likelihood of Ne given data on two temporally spaced genetic samples. The statistical model used is based on the coalescent of the gene copies drawn in the second sample, as described in Berthier et al. (Genetics 2003, 160:741-51). The Monte Carlo computations to compute the likelihood, however, were developed by Eric Anderson, and are orders of magnitude faster than previous implementations.
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Anderson, E. C.2005.
An efficient Monte Carlo method for estimating Ne from temporally spaced samples using a coalescent-based likelihood.