SimRA (Simulation based on Random-graphs Algorithms) is a framework for simulating generic and complex evolutionary scenarios of multiple populations with subdivision and admixture. The algorithm generates a network structure, called Ancestral Recombination Graph (ARG), that models coalescence and genetic exchange events (recombinations) with SNP.
An earlier version of our framework described in Carrieri et al (BioInformatics, 2015) and available here considered only the case of neutral scenario (where also STR polymorphisms can be generated). Recently, we extend the algorithm, sSimRA, that build multiple loci (k) selection, with multiway (k-way) epistasis for any arbitrary k, based on: (1) forward (fwd-SimRA) and (2) backward (back-SimRA) simulation.
git clone git://github.com/ComputationalGenomics/SimRAPlease cite the following article if you use sSimRA (backwards or forward) in your research:
A. Bose, F. Utro, D. Platt, L. Parida. Multiway epistasis simulations for ARG sampling of multiple populations. (submitted)
and/or (for the neutral scenario):
A.P. Carrieri, F. Utro, L. Parida. Sampling ARG of multiple populations under complex configurations of subdivision and admixture. Bioinformatics, 2015.
We welcome contributions but request that you follow the guidelines indicated here.
Copyright 2015 IBM Corporation
Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.
If you have suggestions, questions or comments regarding SimRA, please email us to:
pa_ri_da (at) us.ibm.com (remove the underscores)
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