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July 10, 2019 17:46
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Divergence of two populations with msprime.
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| "import msprime\n", | |
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| "two populations, one splitting off another" | |
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| "pop0 = msprime.PopulationConfiguration(sample_size=3, initial_size = 500, growth_rate = 0.00)\n", | |
| "pop1 = msprime.PopulationConfiguration(sample_size=3, initial_size = 500, growth_rate = 0.00)\n", | |
| "\n", | |
| "demographic_events_ex = [\n", | |
| " msprime.MassMigration(time = 1000, source = 1, dest = 0, proportion = 1)]\n", | |
| "\n", | |
| "ts = msprime.simulate(\n", | |
| " population_configurations = [pop0, pop1], \n", | |
| " length = 1e4, \n", | |
| " demographic_events = demographic_events_ex, \n", | |
| " recombination_rate = 1e-7\n", | |
| ")\n", | |
| "\n", | |
| "colour_map = {0:\"red\", 1:\"blue\"}\n", | |
| "node_colours = {u.id: colour_map[u.population] for u in ts.nodes()}\n", | |
| "\n", | |
| "for tree in ts.trees():\n", | |
| " display(SVG(tree.draw(node_colours=node_colours)))" | |
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| { | |
| "cell_type": "code", | |
| "execution_count": null, | |
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| { | |
| "cell_type": "markdown", | |
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| "source": [ | |
| "two populations diverging from an ancestral population" | |
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| { | |
| "cell_type": "code", | |
| "execution_count": 3, | |
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| ], | |
| "source": [ | |
| "pop0 = msprime.PopulationConfiguration(sample_size=3, initial_size = 500, growth_rate = 0.00)\n", | |
| "pop1 = msprime.PopulationConfiguration(sample_size=3, initial_size = 500, growth_rate = 0.00)\n", | |
| "pop2 = msprime.PopulationConfiguration(sample_size=0, initial_size = 500, growth_rate = 0.00)\n", | |
| "\n", | |
| "demographic_events_ex = [\n", | |
| " msprime.MassMigration(time = 1000, source = 0, dest = 2, proportion = 1),\n", | |
| " msprime.MassMigration(time = 1000, source = 1, dest = 2, proportion = 1)]\n", | |
| "\n", | |
| "ts = msprime.simulate(\n", | |
| " population_configurations = [pop0, pop1, pop2], \n", | |
| " length = 1e4, \n", | |
| " demographic_events = demographic_events_ex, \n", | |
| " recombination_rate = 1e-7\n", | |
| ")\n", | |
| "\n", | |
| "colour_map = {0:\"red\", 1:\"blue\", 2:\"green\"}\n", | |
| "node_colours = {u.id: colour_map[u.population] for u in ts.nodes()}\n", | |
| "\n", | |
| "for tree in ts.trees():\n", | |
| " display(SVG(tree.draw(node_colours=node_colours)))" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": null, | |
| "metadata": {}, | |
| "outputs": [], | |
| "source": [] | |
| } | |
| ], | |
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| "kernelspec": { | |
| "display_name": "Python 3", | |
| "language": "python", | |
| "name": "python3" | |
| }, | |
| "language_info": { | |
| "codemirror_mode": { | |
| "name": "ipython", | |
| "version": 3 | |
| }, | |
| "file_extension": ".py", | |
| "mimetype": "text/x-python", | |
| "name": "python", | |
| "nbconvert_exporter": "python", | |
| "pygments_lexer": "ipython3", | |
| "version": "3.7.3" | |
| } | |
| }, | |
| "nbformat": 4, | |
| "nbformat_minor": 2 | |
| } |
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