 | simuPOPForward-time population genetics simulation environment |
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simuPOP Description
Forward-time population genetics simulation environment simuPOP is a forward-time population genetics simulation module written in Python. The core of simuPOP is a scripting language (Python) that provides a large number of objects and functions to manipulate populations, and a mechanism to evolve populations forward in time.Using this R/Splus-like environment, users can create, manipulate and evolve populations interactively, or write a script and run it as a batch file. Owing to its flexible and extensible design, simuPOP can simulate large and complex evolutionary processes with ease.At a more user-friendly level, simuPOP provides an increasing number of built-in scripts that perform simulations ranging from implementation of basic population genetics models to generating datasets under complex evolutionary scenarios. Requirements: · Python What's New in This Release: · BUG: Fix a bug with population::removeLoci when given keep loci are not in order. · NEW: Prevent the use of greater than one probabilities in Bernulli trails. · NEW: Add a Tkinter implementation for simuProgress. · BUG: Fix a bug where subpopulation names of merged population are not properly merged. · NEW: Allow specifying non-string values in 'chooseFrom' and 'chooseOneOf' in simuOpt parameter specification. · NEW: Allow operators to output to a Python function. · NEW: Allow the use of double-click to open a browse dialog for file and directory input in simuOpt. · BUG: Fix a memory leak bug related to infoEval and infoExec. Optimize infoExec for some simple statements. · CHG: change parameter formOffGenotype of pyOperator to isTransmitter as a result of merging concepts 'primary during mating operator' and 'genotype transmitter'. · CHG: Move all scripts under the scripts directory to online cookbook. · CHG: Change relatedness calculations in operator stat. · NEW: Add calculation of HWE p-value to the stat operator. · NEW: Test individual index in population::removeIndividuals · BUG: Fix a bug when no subpopulation is given in splitSubPops. · CHG: Merge stat(association) to stat(LD), in preparation for case-control association tests. · NEW: (experimental) Add case/control association chisq test to stat. · NEW: (experimental) Add Tajima's pi statistics (mean pairwise difference) to the stat() operator.
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