A Bayesian method for estimating self-fertilization rates and other mating system parameters
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README.md

Bayesian Estimator of Selfing (BES)

BES is a software package for estimating self-fertilization (selfing) rates and other mating system parameters from genotype data. BES estimates parameters in a Bayesian framework using Markov chain Monte Carlo (MCMC). BES contains models of pure hermaphroditism, androdioecy (hermaphrodites + males), and gynodioecy (hermaphrodites + females). Under each model, BES estimates selfing rates, mutation rates, and mating-system specific parameters. BES also contains a generic model for estimating selfing rates and mutation rates independent of a mating system. Additional non-genetic information, such as field observations of the number of females or males, is required for estimating parameters under the gynodioecious model and the androdioecious model.

BES is run as a Unix command line program. It is not a GUI program; instead you must run it in a terminal. Therefore, you might want to keep a Unix Tutorial or Unix cheat sheet handy while you work.

BES runs on Linux, Mac OS X, and Windows. BES is distributed as an extension package for the BAli-Phy inference framework. You might therefore wish to refer to the BAli-Phy Documentation as well.

BES contains a number of modules that correspond to different mating system models. Each model allows estimating a different set of parameters. The generic model and the pure hermaphrodite model without inbreeding depression can be run without modification to estimate the selfing rate and locus-specific mutation rates.

However, the gynodioecious model and the androdiecious model require additional information besides the genetic data, such as (for example) field observations on the fraction of hermaphrodites. Therefore, the user must edit these modules to add this information before attempting to run these models. This manual describes how to add information, but is not a substitute for understanding something about the structure of the model.

For further instructions in installation and usage, see the README.pdf