simuPOP Free and open source forward-time population genetics simulation environment
Download

simuPOP Ranking & Summary

simuPOP Tags

simulate simulator simulation simulate population genetic simulation population simulator

simuPOP Description

Free and open source forward-time population genetics simulation environment simuPOP evolves population(s) forward in time - subject to arbitrary number of genetic and environmental forces (recombination, migration, mutation, population size change etc.). Easy simulations like most models in standard population genetics books can be setup easily, whereas very complicated simulations such as spreading of complex diseases, ancient out-of-africa migrations can be built step by step by adding appropriate operators (objects that work on populations). Requirements: · Python What's New in This Release: · BUG: Fix a memory leak bug in pyParentsChooser. · CHG: mapSelector now accepts a dictionary of tuples, instead of strings. · CHG: mapPenetrance now accepts a dictionary of tuples, instead of strings. · CHG: Remove function individual.intInfo. · CHG: cloneGenoTransmitter accepts a list of information fields to be copied from parents to offspring. Default to all information fields. · CHG: Remove the stage feature of operators. Instead, operators should be passed explicitly to parameters preOps, duringOps, postOps of the evolve function. The existing preOps and postOps parameters are renamed to initOps and finalOps. · CHG: The second parameter of a demographic function is now the parental population itself, instead of parental population sizes. · CHG: Treat ancGen in population.indByID as suggested generation and will continue to check other generations if an individual with specified ID is not found in the suggested generation. · CHG: separate additional fields from infoFields to paramFields in operator pySelector. · CHG: Change parameter selectors to ops in operator pySelector. · CHG: Add support for virtual subpopulations to all penetrance operators. · CHG: Change parameter subPop to subPops in mating schemes. · CHG: Remove all quantitative trait opeartors except pyQuanTrait. Mofidy the interface of pyQuanTrait so that it can handle multiple trait fields and be applied during mating. · CHG: More sampling operators and functions to submodule sampling. · NEW: during-mating operators used in a mating scheme now supports parameters begin, step, end, at and reps. · NEW: add parameter vspMap to combinedSplitter that can define VSPs by union of VSPs. · NEW: add parameter ranges to infoSplitter. · NEW: add productSplitter that define VSPs by intersections of VSPs. · NEW: allow access individual information fields as attributes. · NEW: Add Chi-Squared distribution to the RNG() class. Remove some rarely used memeber functions of this class. · NEW: Allow selectors to be applied during mating to allow for natural selection through the selection of offspring. · NEW: Allow the specification of VSP names in splitters. · NEW: Add parameter freq to operator initByValue. · NEW: Add parameter maleProp to operator initSex. · NEW: Add support for haplodiploid population and sex chromosomes to mapSelector. · NEW: Add support of haploid population to maSelector.

simuPOP Related Software