The clonalescent

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The Clonalescent uses the coalescent model to infer the population sex rate, the expected number of unique individuals, and the statistic Dpsi (useful for detecting deviations from the neutral model). These parameters are inferred from user input genotype frequency spectrums, the program then uses simulations under the Coalescent Model, Markov Chain Monte Carlo and Bayesian estimation to return posterior density distributions for the inferred perimeters. 

To get started, the user will need a genotype frequency spectrum (GFS) from a population of interest. The GFS is a vector with each entry being the number of observations of each unique genotype in a sample. The length of the GFS will then be the number of unique genotypes (u) and the sum of the GFS will be the number of samples (n). The GFS is the basic input format for the Clonalescent which will then return the population sex rate and Dpsi as output.

Optionally, the user can then input a larger sample size (N) and the Clonalescent will calculate the number of unique individuals expected in a sample of that size ( E[Ng} ). We envision multiple uses for this feature and depending on the motivation for the chosen value of N  the resulting output can have a variety of interpretations. A few examples: The user may have an estimate of the census size of a population (Nc), in which case inputting this value will return an E[Ng] that reflects the expected number of unique individuals in the full population. Alternatively, the user may have an estimate of the effective population size (Ne), perhaps even from the same data that was used to generate the GFS, inputting this value will return an E[Ng] that reflects the effective number of unique individuals in the population (Nue). Finally, the user may simply wish to explore how many unique individuals they might expect to find if they altered their sample size, in which case inputting the new sample size will return the E[Ng] value for that new sample size. 

The Clonalescent can also be used in the reverse direction to simulate genotype frequency spectrums given values of Ne, Nue and n. 

For a full description of the Clonalescent please see the download page linked above, a complete description of the underlying theory is given in Wham, Fuller and LaJeunesse. (2015 ) The Coalescent Theory of Clonal Organisms. (In prep. but available shortly) Until then, please do not hesitate to contact the author about any aspect of the Clonalescent, implementation, theory, interpretation or otherwise: Fcwham (at) gmail (dot) com.