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<!DOCTYPE html>
<html class="writer-html5" lang="en" >
<head>
<meta charset="utf-8" /><meta name="generator" content="Docutils 0.17.1: http://docutils.sourceforge.net/" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>Catalog — stdpopsim 0.2.0 documentation</title>
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</head>
<body class="wy-body-for-nav">
<div class="wy-grid-for-nav">
<nav data-toggle="wy-nav-shift" class="wy-nav-side">
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<a href="index.html" class="icon icon-home"> stdpopsim
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</div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
<p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
<ul class="current">
<li class="toctree-l1"><a class="reference internal" href="introduction.html">Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="installation.html">Installation</a></li>
<li class="toctree-l1 current"><a class="current reference internal" href="#">Catalog</a><ul>
<li class="toctree-l2"><a class="reference internal" href="#sec_catalog_AedAeg">Aedes aegypti</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#sec_catalog_AedAeg_genome">Genome</a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="#sec_catalog_AnaPla">Anas platyrhynchos</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#sec_catalog_AnaPla_genome">Genome</a></li>
<li class="toctree-l3"><a class="reference internal" href="#sec_catalog_AnaPla_models">Demographic Models</a><ul>
<li class="toctree-l4"><a class="reference internal" href="#sec_catalog_anapla_models_mallardblackduck_2l19">North American Mallard/Black Duck split</a></li>
</ul>
</li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="#sec_catalog_AnoCar">Anolis carolinensis</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#sec_catalog_AnoCar_genome">Genome</a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="#sec_catalog_AnoGam">Anopheles gambiae</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#sec_catalog_AnoGam_genome">Genome</a></li>
<li class="toctree-l3"><a class="reference internal" href="#sec_catalog_AnoGam_models">Demographic Models</a><ul>
<li class="toctree-l4"><a class="reference internal" href="#sec_catalog_anogam_models_gabonag1000g_1a17">Stairwayplot estimates of N(t) for Gabon sample</a></li>
</ul>
</li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="#sec_catalog_ApiMel">Apis mellifera</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#sec_catalog_ApiMel_genome">Genome</a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="#sec_catalog_AraTha">Arabidopsis thaliana</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#sec_catalog_AraTha_genome">Genome</a></li>
<li class="toctree-l3"><a class="reference internal" href="#sec_catalog_AraTha_genetic_maps">Genetic Maps</a><ul>
<li class="toctree-l4"><a class="reference internal" href="#sec_catalog_aratha_genetic_maps_salomeaveraged_tair10">SalomeAveraged_TAIR10</a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="#sec_catalog_AraTha_models">Demographic Models</a><ul>
<li class="toctree-l4"><a class="reference internal" href="#sec_catalog_aratha_models_southmiddleatlas_1d17">South Middle Atlas piecewise constant size</a></li>
<li class="toctree-l4"><a class="reference internal" href="#sec_catalog_aratha_models_african2epoch_1h18">South Middle Atlas African two epoch model</a></li>
<li class="toctree-l4"><a class="reference internal" href="#sec_catalog_aratha_models_african3epoch_1h18">South Middle Atlas African three epoch model</a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="#sec_catalog_AraTha_annotations">Annotations</a><ul>
<li class="toctree-l4"><a class="reference internal" href="#sec_catalog_aratha_annotations_araport_11_exons">araport_11_exons</a></li>
<li class="toctree-l4"><a class="reference internal" href="#sec_catalog_aratha_annotations_araport_11_cds">araport_11_CDS</a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="#sec_catalog_AraTha_dfe">Distribution of Fitness Effects (DFEs)</a><ul>
<li class="toctree-l4"><a class="reference internal" href="#sec_catalog_aratha_dfes_gamma_h18">Gamma_H18</a></li>
</ul>
</li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="#sec_catalog_BosTau">Bos taurus</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#sec_catalog_BosTau_genome">Genome</a></li>
<li class="toctree-l3"><a class="reference internal" href="#sec_catalog_BosTau_models">Demographic Models</a><ul>
<li class="toctree-l4"><a class="reference internal" href="#sec_catalog_bostau_models_holsteinfriesian_1m13">Piecewise size changes in Holstein-Friesian cattle.</a></li>
</ul>
</li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="#sec_catalog_CaeEle">Caenorhabditis elegans</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#sec_catalog_CaeEle_genome">Genome</a></li>
<li class="toctree-l3"><a class="reference internal" href="#sec_catalog_CaeEle_genetic_maps">Genetic Maps</a><ul>
<li class="toctree-l4"><a class="reference internal" href="#sec_catalog_caeele_genetic_maps_rockmanriail_ce11">RockmanRIAIL_ce11</a></li>
</ul>
</li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="#sec_catalog_CanFam">Canis familiaris</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#sec_catalog_CanFam_genome">Genome</a></li>
<li class="toctree-l3"><a class="reference internal" href="#sec_catalog_CanFam_genetic_maps">Genetic Maps</a><ul>
<li class="toctree-l4"><a class="reference internal" href="#sec_catalog_canfam_genetic_maps_campbell2016_canfam3_1">Campbell2016_CanFam3_1</a></li>
</ul>
</li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="#sec_catalog_ChlRei">Chlamydomonas reinhardtii</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#sec_catalog_ChlRei_genome">Genome</a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="#sec_catalog_DroMel">Drosophila melanogaster</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#sec_catalog_DroMel_genome">Genome</a></li>
<li class="toctree-l3"><a class="reference internal" href="#sec_catalog_DroMel_genetic_maps">Genetic Maps</a><ul>
<li class="toctree-l4"><a class="reference internal" href="#sec_catalog_dromel_genetic_maps_comeroncrossover_dm6">ComeronCrossover_dm6</a></li>
<li class="toctree-l4"><a class="reference internal" href="#sec_catalog_dromel_genetic_maps_comeroncrossoverv2_dm6">ComeronCrossoverV2_dm6</a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="#sec_catalog_DroMel_models">Demographic Models</a><ul>
<li class="toctree-l4"><a class="reference internal" href="#sec_catalog_dromel_models_african3epoch_1s16">Three epoch African population</a></li>
<li class="toctree-l4"><a class="reference internal" href="#sec_catalog_dromel_models_outofafrica_2l06">Three epoch model for African and European populations</a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="#sec_catalog_DroMel_annotations">Annotations</a><ul>
<li class="toctree-l4"><a class="reference internal" href="#sec_catalog_dromel_annotations_flybase_bdgp6.32.51_exons">FlyBase_BDGP6.32.51_exons</a></li>
<li class="toctree-l4"><a class="reference internal" href="#sec_catalog_dromel_annotations_flybase_bdgp6.32.51_cds">FlyBase_BDGP6.32.51_CDS</a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="#sec_catalog_DroMel_dfe">Distribution of Fitness Effects (DFEs)</a><ul>
<li class="toctree-l4"><a class="reference internal" href="#sec_catalog_dromel_dfes_gamma_h17">Gamma_H17</a></li>
<li class="toctree-l4"><a class="reference internal" href="#sec_catalog_dromel_dfes_lognormalpluspositive_r16">LognormalPlusPositive_R16</a></li>
</ul>
</li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="#sec_catalog_DroSec">Drosophila sechellia</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#sec_catalog_DroSec_genome">Genome</a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="#sec_catalog_EscCol">Escherichia coli</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#sec_catalog_EscCol_genome">Genome</a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="#sec_catalog_GasAcu">Gasterosteus aculeatus</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#sec_catalog_GasAcu_genome">Genome</a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="#sec_catalog_HelAnn">Helianthus annuus</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#sec_catalog_HelAnn_genome">Genome</a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="#sec_catalog_HelMel">Heliconius melpomene</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#sec_catalog_HelMel_genome">Genome</a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="#sec_catalog_HomSap">Homo sapiens</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#sec_catalog_HomSap_genome">Genome</a></li>
<li class="toctree-l3"><a class="reference internal" href="#sec_catalog_HomSap_genetic_maps">Genetic Maps</a><ul>
<li class="toctree-l4"><a class="reference internal" href="#sec_catalog_homsap_genetic_maps_hapmapii_grch37">HapMapII_GRCh37</a></li>
<li class="toctree-l4"><a class="reference internal" href="#sec_catalog_homsap_genetic_maps_hapmapii_grch38">HapMapII_GRCh38</a></li>
<li class="toctree-l4"><a class="reference internal" href="#sec_catalog_homsap_genetic_maps_decodesexaveraged_grch36">DeCodeSexAveraged_GRCh36</a></li>
<li class="toctree-l4"><a class="reference internal" href="#sec_catalog_homsap_genetic_maps_decodesexaveraged_grch38">DeCodeSexAveraged_GRCh38</a></li>
<li class="toctree-l4"><a class="reference internal" href="#sec_catalog_homsap_genetic_maps_pyrhoacb_grch38">PyrhoACB_GRCh38</a></li>
<li class="toctree-l4"><a class="reference internal" href="#sec_catalog_homsap_genetic_maps_pyrhoasw_grch38">PyrhoASW_GRCh38</a></li>
<li class="toctree-l4"><a class="reference internal" href="#sec_catalog_homsap_genetic_maps_pyrhobeb_grch38">PyrhoBEB_GRCh38</a></li>
<li class="toctree-l4"><a class="reference internal" href="#sec_catalog_homsap_genetic_maps_pyrhocdx_grch38">PyrhoCDX_GRCh38</a></li>
<li class="toctree-l4"><a class="reference internal" href="#sec_catalog_homsap_genetic_maps_pyrhoceu_grch38">PyrhoCEU_GRCh38</a></li>
<li class="toctree-l4"><a class="reference internal" href="#sec_catalog_homsap_genetic_maps_pyrhochb_grch38">PyrhoCHB_GRCh38</a></li>
<li class="toctree-l4"><a class="reference internal" href="#sec_catalog_homsap_genetic_maps_pyrhochs_grch38">PyrhoCHS_GRCh38</a></li>
<li class="toctree-l4"><a class="reference internal" href="#sec_catalog_homsap_genetic_maps_pyrhoclm_grch38">PyrhoCLM_GRCh38</a></li>
<li class="toctree-l4"><a class="reference internal" href="#sec_catalog_homsap_genetic_maps_pyrhoesn_grch38">PyrhoESN_GRCh38</a></li>
<li class="toctree-l4"><a class="reference internal" href="#sec_catalog_homsap_genetic_maps_pyrhofin_grch38">PyrhoFIN_GRCh38</a></li>
<li class="toctree-l4"><a class="reference internal" href="#sec_catalog_homsap_genetic_maps_pyrhogbr_grch38">PyrhoGBR_GRCh38</a></li>
<li class="toctree-l4"><a class="reference internal" href="#sec_catalog_homsap_genetic_maps_pyrhogih_grch38">PyrhoGIH_GRCh38</a></li>
<li class="toctree-l4"><a class="reference internal" href="#sec_catalog_homsap_genetic_maps_pyrhogwd_grch38">PyrhoGWD_GRCh38</a></li>
<li class="toctree-l4"><a class="reference internal" href="#sec_catalog_homsap_genetic_maps_pyrhoibs_grch38">PyrhoIBS_GRCh38</a></li>
<li class="toctree-l4"><a class="reference internal" href="#sec_catalog_homsap_genetic_maps_pyrhoitu_grch38">PyrhoITU_GRCh38</a></li>
<li class="toctree-l4"><a class="reference internal" href="#sec_catalog_homsap_genetic_maps_pyrhojpt_grch38">PyrhoJPT_GRCh38</a></li>
<li class="toctree-l4"><a class="reference internal" href="#sec_catalog_homsap_genetic_maps_pyrhokhv_grch38">PyrhoKHV_GRCh38</a></li>
<li class="toctree-l4"><a class="reference internal" href="#sec_catalog_homsap_genetic_maps_pyrholwk_grch38">PyrhoLWK_GRCh38</a></li>
<li class="toctree-l4"><a class="reference internal" href="#sec_catalog_homsap_genetic_maps_pyrhomsl_grch38">PyrhoMSL_GRCh38</a></li>
<li class="toctree-l4"><a class="reference internal" href="#sec_catalog_homsap_genetic_maps_pyrhomxl_grch38">PyrhoMXL_GRCh38</a></li>
<li class="toctree-l4"><a class="reference internal" href="#sec_catalog_homsap_genetic_maps_pyrhopel_grch38">PyrhoPEL_GRCh38</a></li>
<li class="toctree-l4"><a class="reference internal" href="#sec_catalog_homsap_genetic_maps_pyrhopjl_grch38">PyrhoPJL_GRCh38</a></li>
<li class="toctree-l4"><a class="reference internal" href="#sec_catalog_homsap_genetic_maps_pyrhopur_grch38">PyrhoPUR_GRCh38</a></li>
<li class="toctree-l4"><a class="reference internal" href="#sec_catalog_homsap_genetic_maps_pyrhostu_grch38">PyrhoSTU_GRCh38</a></li>
<li class="toctree-l4"><a class="reference internal" href="#sec_catalog_homsap_genetic_maps_pyrhotsi_grch38">PyrhoTSI_GRCh38</a></li>
<li class="toctree-l4"><a class="reference internal" href="#sec_catalog_homsap_genetic_maps_pyrhoyri_grch38">PyrhoYRI_GRCh38</a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="#sec_catalog_HomSap_models">Demographic Models</a><ul>
<li class="toctree-l4"><a class="reference internal" href="#sec_catalog_homsap_models_outofafricaextendedneandertaladmixturepulse_3i21">Three population out-of-Africa with an extended pulse of Neandertal admixture into Europeans</a></li>
<li class="toctree-l4"><a class="reference internal" href="#sec_catalog_homsap_models_outofafrica_3g09">Three population out-of-Africa</a></li>
<li class="toctree-l4"><a class="reference internal" href="#sec_catalog_homsap_models_outofafrica_2t12">Two population out-of-Africa</a></li>
<li class="toctree-l4"><a class="reference internal" href="#sec_catalog_homsap_models_africa_1t12">African population</a></li>
<li class="toctree-l4"><a class="reference internal" href="#sec_catalog_homsap_models_americanadmixture_4b11">American admixture</a></li>
<li class="toctree-l4"><a class="reference internal" href="#sec_catalog_homsap_models_outofafricaarchaicadmixture_5r19">Three population out-of-Africa with archaic admixture</a></li>
<li class="toctree-l4"><a class="reference internal" href="#sec_catalog_homsap_models_zigzag_1s14">Periodic growth and decline.</a></li>
<li class="toctree-l4"><a class="reference internal" href="#sec_catalog_homsap_models_ancienteurasia_9k19">Multi-population model of ancient Eurasia</a></li>
<li class="toctree-l4"><a class="reference internal" href="#sec_catalog_homsap_models_papuansoutofafrica_10j19">Out-of-Africa with archaic admixture into Papuans</a></li>
<li class="toctree-l4"><a class="reference internal" href="#sec_catalog_homsap_models_ashksub_7g19">Ashkenazi Jewish with substructure and European admixture</a></li>
<li class="toctree-l4"><a class="reference internal" href="#sec_catalog_homsap_models_outofafrica_4j17">4 population out of Africa</a></li>
<li class="toctree-l4"><a class="reference internal" href="#sec_catalog_homsap_models_africa_1b08">African-americans population</a></li>
<li class="toctree-l4"><a class="reference internal" href="#sec_catalog_homsap_models_ancienteurope_4a21">Multi-population model of ancient Europe</a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="#sec_catalog_HomSap_annotations">Annotations</a><ul>
<li class="toctree-l4"><a class="reference internal" href="#sec_catalog_homsap_annotations_ensembl_havana_104_exons">ensembl_havana_104_exons</a></li>
<li class="toctree-l4"><a class="reference internal" href="#sec_catalog_homsap_annotations_ensembl_havana_104_cds">ensembl_havana_104_CDS</a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="#sec_catalog_HomSap_dfe">Distribution of Fitness Effects (DFEs)</a><ul>
<li class="toctree-l4"><a class="reference internal" href="#sec_catalog_homsap_dfes_gamma_k17">Gamma_K17</a></li>
<li class="toctree-l4"><a class="reference internal" href="#sec_catalog_homsap_dfes_gamma_h17">Gamma_H17</a></li>
</ul>
</li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="#sec_catalog_PanTro">Pan troglodytes</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#sec_catalog_PanTro_genome">Genome</a></li>
<li class="toctree-l3"><a class="reference internal" href="#sec_catalog_PanTro_models">Demographic Models</a><ul>
<li class="toctree-l4"><a class="reference internal" href="#sec_catalog_pantro_models_bonoboghost_4k19">Ghost admixture into bonobos</a></li>
</ul>
</li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="#sec_catalog_PapAnu">Papio anubis</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#sec_catalog_PapAnu_genome">Genome</a></li>
<li class="toctree-l3"><a class="reference internal" href="#sec_catalog_PapAnu_genetic_maps">Genetic Maps</a><ul>
<li class="toctree-l4"><a class="reference internal" href="#sec_catalog_papanu_genetic_maps_pyrho_panubis1_0">Pyrho_PAnubis1_0</a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="#sec_catalog_PapAnu_models">Demographic Models</a><ul>
<li class="toctree-l4"><a class="reference internal" href="#sec_catalog_papanu_models_singlepopsmcpp_1w22">SMC++ estimates of N(t) for Papio Anubis individuals</a></li>
</ul>
</li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="#sec_catalog_PonAbe">Pongo abelii</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#sec_catalog_PonAbe_genome">Genome</a></li>
<li class="toctree-l3"><a class="reference internal" href="#sec_catalog_PonAbe_genetic_maps">Genetic Maps</a><ul>
<li class="toctree-l4"><a class="reference internal" href="#sec_catalog_ponabe_genetic_maps_naterpa_ponabe3">NaterPA_PonAbe3</a></li>
<li class="toctree-l4"><a class="reference internal" href="#sec_catalog_ponabe_genetic_maps_naterpp_ponabe3">NaterPP_PonAbe3</a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="#sec_catalog_PonAbe_models">Demographic Models</a><ul>
<li class="toctree-l4"><a class="reference internal" href="#sec_catalog_ponabe_models_twospecies_2l11">Two population orangutan model</a></li>
</ul>
</li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="#sec_catalog_StrAga">Streptococcus agalactiae</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#sec_catalog_StrAga_genome">Genome</a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="#generic-models">Generic models</a></li>
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<li class="toctree-l1"><a class="reference internal" href="tutorial.html">Tutorials</a></li>
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<section id="catalog">
<span id="sec-catalog"></span><h1>Catalog<a class="headerlink" href="#catalog" title="Permalink to this headline"></a></h1>
<p>With <code class="docutils literal notranslate"><span class="pre">stdpopsim</span></code>, you can run simulations from a number of demographic models
that were implemented from published demographic histories. These models have been
rigorously checked and tested by multiple people, so you can rest easy knowing that
your simulations are reproducible and bug-free!</p>
<p>This catalog shows you all of the possible options that you can use to configure
your simulation.
It is organised around a number of choices that you’ll need to make about the
<a class="reference internal" href="api.html#stdpopsim.Species" title="stdpopsim.Species"><code class="xref py py-class docutils literal notranslate"><span class="pre">Species</span></code></a> you wish to simulate:</p>
<ol class="arabic simple">
<li><p>Which <strong>chromosome</strong>? (ie. which <a class="reference internal" href="api.html#stdpopsim.Genome" title="stdpopsim.Genome"><code class="xref py py-class docutils literal notranslate"><span class="pre">Genome</span></code></a> object?)</p></li>
<li><p>Which <strong>genetic map</strong>? (ie. which <code class="xref py py-class docutils literal notranslate"><span class="pre">GeneticMap</span></code> object?)</p></li>
<li><p>Which <strong>model of demographic history</strong>? (ie. which <a class="reference internal" href="api.html#stdpopsim.DemographicModel" title="stdpopsim.DemographicModel"><code class="xref py py-class docutils literal notranslate"><span class="pre">DemographicModel</span></code></a> object)</p></li>
<li><p>Which <strong>distribution of fitness effects</strong> (ie. which <a class="reference internal" href="api.html#stdpopsim.DFE" title="stdpopsim.DFE"><code class="xref py py-class docutils literal notranslate"><span class="pre">DFE</span></code></a> object) within</p></li>
<li><p>which <strong>annotation track</strong>? (ie. which <a class="reference internal" href="api.html#stdpopsim.Annotation" title="stdpopsim.Annotation"><code class="xref py py-class docutils literal notranslate"><span class="pre">Annotation</span></code></a> object)</p></li>
</ol>
<p>For instance, suppose you are interested in simulating modern human samples of</p>
<ol class="arabic simple">
<li><p>chromosome 22, using</p></li>
<li><p>the HapMapII genetic map, under</p></li>
<li><p>a 3-population Out-of-Africa model, with</p></li>
<li><p>background selection acting within</p></li>
<li><p>exons from the Ensembl Havana 104 annotations.</p></li>
</ol>
<p>The following command simulates 2 samples from each of the three populations,
(named YRI, CEU, and CHB) and saves the output to a file called <code class="docutils literal notranslate"><span class="pre">test.trees</span></code>:</p>
<div class="highlight-console notranslate"><div class="highlight"><pre><span></span><span class="gp">$ </span>stdpopsim -e slim HomSap -c chr22 -o test.trees -g HapMapII_GRCh38 <span class="se">\</span>
<span class="gp">$ </span>--dfe Gamma_K17 --dfe-annotation ensembl_havana_104_exons <span class="se">\</span>
<span class="gp">$ </span>-d OutOfAfrica_3G09 YRI:2 CEU:2 CHB:2
</pre></div>
</div>
<p>(To learn more about using <code class="docutils literal notranslate"><span class="pre">stdpopsim</span></code> via the command-line, read our
<a class="reference internal" href="tutorial.html#sec-cli-tute"><span class="std std-ref">tutorial</span></a> about it.)</p>
<p>Are there other well-known organisms, genetic maps or models that
you’d like to see in <code class="docutils literal notranslate"><span class="pre">stdpopsim</span></code>? Head to our <a class="reference internal" href="development.html#sec-development"><span class="std std-ref">Development</span></a>
page to learn about the process for adding new items to the catalog.
Then, if you feel ready, make an issue on our
<a class="reference external" href="https://github.com/popgensims/stdpopsim/issues">GitHub page</a>.</p>
<section id="sec_catalog_AedAeg">
<span id="sec_catalog_AedAeg"></span><h2>Aedes aegypti<a class="headerlink" href="#sec_catalog_AedAeg" title="Permalink to this headline"></a></h2>
<dl class="field-list simple">
<dt class="field-odd">ID</dt>
<dd class="field-odd"><p>AedAeg</p>
</dd>
<dt class="field-even">Name</dt>
<dd class="field-even"><p>Aedes aegypti</p>
</dd>
<dt class="field-odd">Common name</dt>
<dd class="field-odd"><p>Yellow fever mosquito</p>
</dd>
<dt class="field-even">Generation time</dt>
<dd class="field-even"><p>0.06666666666666667 (<a class="reference external" href="https://doi.org/10.1186/s12915-017-0351-0">Crawford et al., 2017</a>)</p>
</dd>
<dt class="field-odd">Population size</dt>
<dd class="field-odd"><p>1000000.0 (<a class="reference external" href="https://doi.org/10.1186/s12915-017-0351-0">Crawford et al., 2017</a>)</p>
</dd>
</dl>
<section id="sec_catalog_AedAeg_genome">
<h3>Genome<a class="headerlink" href="#sec_catalog_AedAeg_genome" title="Permalink to this headline"></a></h3>
<table class="docutils align-default">
<colgroup>
<col style="width: 25%" />
<col style="width: 25%" />
<col style="width: 25%" />
<col style="width: 25%" />
</colgroup>
<thead>
<tr class="row-odd"><th class="head"><p>ID</p></th>
<th class="head"><p>Length</p></th>
<th class="head"><p>Recombination rate</p></th>
<th class="head"><p>Mutation rate</p></th>
</tr>
</thead>
<tbody>
<tr class="row-even"><td><p>1</p></td>
<td><p>310827022</p></td>
<td><p>3.06e-09</p></td>
<td><p>3.5e-09</p></td>
</tr>
<tr class="row-odd"><td><p>2</p></td>
<td><p>474425716</p></td>
<td><p>2.49e-09</p></td>
<td><p>3.5e-09</p></td>
</tr>
<tr class="row-even"><td><p>3</p></td>
<td><p>409777670</p></td>
<td><p>2.91e-09</p></td>
<td><p>3.5e-09</p></td>
</tr>
<tr class="row-odd"><td><p>MT</p></td>
<td><p>16790</p></td>
<td><p>0</p></td>
<td><p>3.5e-09</p></td>
</tr>
</tbody>
</table>
<p>Mutation and recombination rates are in units of per bp and per generation.</p>
</section>
</section>
<hr class="docutils" />
<section id="sec_catalog_AnaPla">
<span id="sec_catalog_AnaPla"></span><h2>Anas platyrhynchos<a class="headerlink" href="#sec_catalog_AnaPla" title="Permalink to this headline"></a></h2>
<dl class="field-list simple">
<dt class="field-odd">ID</dt>
<dd class="field-odd"><p>AnaPla</p>
</dd>
<dt class="field-even">Name</dt>
<dd class="field-even"><p>Anas platyrhynchos</p>
</dd>
<dt class="field-odd">Common name</dt>
<dd class="field-odd"><p>Mallard</p>
</dd>
<dt class="field-even">Generation time</dt>
<dd class="field-even"><p>4 (<a class="reference external" href="https://doi.org/10.1111/mec.15343">Lavretsky et al., 2020</a>)</p>
</dd>
<dt class="field-odd">Population size</dt>
<dd class="field-odd"><p>156000 (<a class="reference external" href="https://doi.org/10.24272/j.issn.2095-8137.2020.133">Guo et al., 2021</a>)</p>
</dd>
</dl>
<section id="sec_catalog_AnaPla_genome">
<h3>Genome<a class="headerlink" href="#sec_catalog_AnaPla_genome" title="Permalink to this headline"></a></h3>
<table class="docutils align-default">
<colgroup>
<col style="width: 25%" />
<col style="width: 25%" />
<col style="width: 25%" />
<col style="width: 25%" />
</colgroup>
<thead>
<tr class="row-odd"><th class="head"><p>ID</p></th>
<th class="head"><p>Length</p></th>
<th class="head"><p>Recombination rate</p></th>
<th class="head"><p>Mutation rate</p></th>
</tr>
</thead>
<tbody>
<tr class="row-even"><td><p>1</p></td>
<td><p>208326429</p></td>
<td><p>1.52e-08</p></td>
<td><p>4.83e-09</p></td>
</tr>
<tr class="row-odd"><td><p>2</p></td>
<td><p>162939446</p></td>
<td><p>1.39e-08</p></td>
<td><p>4.83e-09</p></td>
</tr>
<tr class="row-even"><td><p>3</p></td>
<td><p>119723720</p></td>
<td><p>9.38e-09</p></td>
<td><p>4.83e-09</p></td>
</tr>
<tr class="row-odd"><td><p>4</p></td>
<td><p>77626585</p></td>
<td><p>1.2e-08</p></td>
<td><p>4.83e-09</p></td>
</tr>
<tr class="row-even"><td><p>5</p></td>
<td><p>64988622</p></td>
<td><p>1.21e-08</p></td>
<td><p>4.83e-09</p></td>
</tr>
<tr class="row-odd"><td><p>6</p></td>
<td><p>39543408</p></td>
<td><p>3.04e-08</p></td>
<td><p>4.83e-09</p></td>
</tr>
<tr class="row-even"><td><p>7</p></td>
<td><p>37812880</p></td>
<td><p>2.59e-08</p></td>
<td><p>4.83e-09</p></td>
</tr>
<tr class="row-odd"><td><p>8</p></td>
<td><p>33348632</p></td>
<td><p>1.28e-08</p></td>
<td><p>4.83e-09</p></td>
</tr>
<tr class="row-even"><td><p>9</p></td>
<td><p>26742597</p></td>
<td><p>1.34e-08</p></td>
<td><p>4.83e-09</p></td>
</tr>
<tr class="row-odd"><td><p>10</p></td>
<td><p>22933227</p></td>
<td><p>2.5e-08</p></td>
<td><p>4.83e-09</p></td>
</tr>
<tr class="row-even"><td><p>11</p></td>
<td><p>22193879</p></td>
<td><p>1.5e-08</p></td>
<td><p>4.83e-09</p></td>
</tr>
<tr class="row-odd"><td><p>12</p></td>
<td><p>22338721</p></td>
<td><p>3.15e-08</p></td>
<td><p>4.83e-09</p></td>
</tr>
<tr class="row-even"><td><p>13</p></td>
<td><p>21714986</p></td>
<td><p>1.41e-08</p></td>
<td><p>4.83e-09</p></td>
</tr>
<tr class="row-odd"><td><p>14</p></td>
<td><p>20320564</p></td>
<td><p>8.61e-09</p></td>
<td><p>4.83e-09</p></td>
</tr>
<tr class="row-even"><td><p>15</p></td>
<td><p>18227546</p></td>
<td><p>3.79e-09</p></td>
<td><p>4.83e-09</p></td>
</tr>
<tr class="row-odd"><td><p>16</p></td>
<td><p>16053328</p></td>
<td><p>3.86e-09</p></td>
<td><p>4.83e-09</p></td>
</tr>
<tr class="row-even"><td><p>17</p></td>
<td><p>15319648</p></td>
<td><p>3.13e-09</p></td>
<td><p>4.83e-09</p></td>
</tr>
<tr class="row-odd"><td><p>18</p></td>
<td><p>13333155</p></td>
<td><p>1.58e-09</p></td>
<td><p>4.83e-09</p></td>
</tr>
<tr class="row-even"><td><p>19</p></td>
<td><p>12198306</p></td>
<td><p>1.43e-08</p></td>
<td><p>4.83e-09</p></td>
</tr>
<tr class="row-odd"><td><p>20</p></td>
<td><p>12091001</p></td>
<td><p>1.43e-08</p></td>
<td><p>4.83e-09</p></td>
</tr>
<tr class="row-even"><td><p>21</p></td>
<td><p>8553409</p></td>
<td><p>1.43e-08</p></td>
<td><p>4.83e-09</p></td>
</tr>
<tr class="row-odd"><td><p>22</p></td>
<td><p>16160689</p></td>
<td><p>1.43e-08</p></td>
<td><p>4.83e-09</p></td>
</tr>
<tr class="row-even"><td><p>23</p></td>
<td><p>7977799</p></td>
<td><p>1.43e-08</p></td>
<td><p>4.83e-09</p></td>
</tr>
<tr class="row-odd"><td><p>24</p></td>
<td><p>7737077</p></td>
<td><p>1.43e-08</p></td>
<td><p>4.83e-09</p></td>
</tr>
<tr class="row-even"><td><p>25</p></td>
<td><p>7574731</p></td>
<td><p>1.43e-08</p></td>
<td><p>4.83e-09</p></td>
</tr>
<tr class="row-odd"><td><p>26</p></td>
<td><p>6918023</p></td>
<td><p>1.43e-08</p></td>
<td><p>4.83e-09</p></td>
</tr>
<tr class="row-even"><td><p>27</p></td>
<td><p>6270716</p></td>
<td><p>1.43e-08</p></td>
<td><p>4.83e-09</p></td>
</tr>
<tr class="row-odd"><td><p>28</p></td>
<td><p>5960150</p></td>
<td><p>1.43e-08</p></td>
<td><p>4.83e-09</p></td>
</tr>
<tr class="row-even"><td><p>29</p></td>
<td><p>1456683</p></td>
<td><p>1.43e-08</p></td>
<td><p>4.83e-09</p></td>
</tr>
<tr class="row-odd"><td><p>30</p></td>
<td><p>1872559</p></td>
<td><p>1.43e-08</p></td>
<td><p>4.83e-09</p></td>
</tr>
<tr class="row-even"><td><p>Z</p></td>
<td><p>81233375</p></td>
<td><p>1.43e-08</p></td>
<td><p>4.83e-09</p></td>
</tr>
<tr class="row-odd"><td><p>31</p></td>
<td><p>2637124</p></td>
<td><p>1.43e-08</p></td>
<td><p>4.83e-09</p></td>
</tr>
<tr class="row-even"><td><p>32</p></td>
<td><p>3473573</p></td>
<td><p>1.43e-08</p></td>
<td><p>4.83e-09</p></td>
</tr>
<tr class="row-odd"><td><p>33</p></td>
<td><p>2151773</p></td>
<td><p>1.43e-08</p></td>
<td><p>4.83e-09</p></td>
</tr>
<tr class="row-even"><td><p>34</p></td>
<td><p>7214884</p></td>
<td><p>1.43e-08</p></td>
<td><p>4.83e-09</p></td>
</tr>
<tr class="row-odd"><td><p>35</p></td>
<td><p>5548691</p></td>
<td><p>1.43e-08</p></td>
<td><p>4.83e-09</p></td>
</tr>
<tr class="row-even"><td><p>36</p></td>
<td><p>3997205</p></td>
<td><p>1.43e-08</p></td>
<td><p>4.83e-09</p></td>
</tr>
<tr class="row-odd"><td><p>37</p></td>
<td><p>3148754</p></td>
<td><p>1.43e-08</p></td>
<td><p>4.83e-09</p></td>
</tr>
<tr class="row-even"><td><p>38</p></td>
<td><p>2836164</p></td>
<td><p>1.43e-08</p></td>
<td><p>4.83e-09</p></td>
</tr>
<tr class="row-odd"><td><p>39</p></td>
<td><p>2018729</p></td>
<td><p>1.43e-08</p></td>
<td><p>4.83e-09</p></td>
</tr>
<tr class="row-even"><td><p>40</p></td>
<td><p>1354177</p></td>
<td><p>1.43e-08</p></td>
<td><p>4.83e-09</p></td>
</tr>
</tbody>
</table>
<p>Mutation and recombination rates are in units of per bp and per generation.</p>
</section>
<hr class="docutils" />
<section id="sec_catalog_AnaPla_models">
<h3>Demographic Models<a class="headerlink" href="#sec_catalog_AnaPla_models" title="Permalink to this headline"></a></h3>
<table class="docutils align-default">
<colgroup>
<col style="width: 50%" />
<col style="width: 50%" />
</colgroup>
<thead>
<tr class="row-odd"><th class="head"><p>ID</p></th>
<th class="head"><p>Description</p></th>
</tr>
</thead>
<tbody>
<tr class="row-even"><td><p><a class="reference internal" href="#sec_catalog_anapla_models_mallardblackduck_2l19">MallardBlackDuck_2L19</a></p></td>
<td><p>North American Mallard/Black Duck split</p></td>
</tr>
</tbody>
</table>
<section id="sec_catalog_anapla_models_mallardblackduck_2l19">
<span id="sec_catalog_anapla_models_mallardblackduck_2l19"></span><h4>North American Mallard/Black Duck split<a class="headerlink" href="#sec_catalog_anapla_models_mallardblackduck_2l19" title="Permalink to this headline"></a></h4>
<p>
This is a model fit to contemporary samples of wild North American
mallard and black duck, using the “split-migration” model of dadi.
See Figure 6 of Lavretsky et al 2019.
</p>
<p class="rubric">Details</p>
<dl class="field-list simple">
<dt class="field-odd">ID</dt>
<dd class="field-odd"><p>MallardBlackDuck_2L19</p>
</dd>
<dt class="field-even">Description</dt>
<dd class="field-even"><p>North American Mallard/Black Duck split</p>
</dd>
<dt class="field-odd">Num populations</dt>
<dd class="field-odd"><p>3</p>
</dd>
</dl>
<p class="rubric">Populations</p>
<table class="docutils align-default">
<colgroup>
<col style="width: 25%" />
<col style="width: 25%" />
<col style="width: 25%" />
<col style="width: 25%" />
</colgroup>
<thead>
<tr class="row-odd"><th class="head"><p>Index</p></th>
<th class="head"><p>ID</p></th>
<th class="head"><p>Sampling time</p></th>
<th class="head"><p>Description</p></th>
</tr>
</thead>
<tbody>
<tr class="row-even"><td><p>0</p></td>
<td><p>Mallard</p></td>
<td><p>None</p></td>
<td><p>Wild North American mallards</p></td>
</tr>
<tr class="row-odd"><td><p>1</p></td>
<td><p>Black_duck</p></td>
<td><p>None</p></td>
<td><p>Wild black ducks</p></td>
</tr>
<tr class="row-even"><td><p>2</p></td>
<td><p>Ancestral</p></td>
<td><p>158076.25</p></td>
<td><p>Ancestral population</p></td>
</tr>
</tbody>
</table>
<p class="rubric">Citations</p>
<ul class="simple">
<li><p>Lavretsky et al., 2019. <a class="reference external" href="https://doi.org/10.1111/mec.15343">https://doi.org/10.1111/mec.15343</a></p></li>
</ul>
<p class="rubric">Demographic Model parameters</p>
<table class="docutils align-default">
<colgroup>
<col style="width: 33%" />
<col style="width: 33%" />
<col style="width: 33%" />
</colgroup>
<thead>
<tr class="row-odd"><th class="head"><p>Parameter Type (units)</p></th>
<th class="head"><p>Value</p></th>
<th class="head"><p>Description</p></th>
</tr>
</thead>
<tbody>
<tr class="row-even"><td><p>Population size</p></td>
<td><p>819,535</p></td>
<td><p>Ancestral pop. size</p></td>
</tr>
<tr class="row-odd"><td><p>Population size</p></td>
<td><p>1,570,000</p></td>
<td><p>Mallard pop. size</p></td>
</tr>
<tr class="row-even"><td><p>Population size</p></td>
<td><p>1,370,000</p></td>
<td><p>Black duck pop. size</p></td>
</tr>
<tr class="row-odd"><td><p>Migration rate (x10^-6 per gen.)</p></td>
<td><p>0.84</p></td>
<td><p>Black-Mallard migration rate</p></td>
</tr>
<tr class="row-even"><td><p>Migration rate (x10^-6 per gen.)</p></td>
<td><p>1.10</p></td>
<td><p>Mallard-Black migration rate</p></td>
</tr>
<tr class="row-odd"><td><p>Epoch Time (gen.)</p></td>
<td><p>158076</p></td>
<td><p>Mallard/Black split time</p></td>
</tr>
<tr class="row-even"><td><p>Generation time (yrs.)</p></td>
<td><p>4</p></td>
<td><p>Generation time</p></td>
</tr>
<tr class="row-odd"><td><p>Mutation rate (subst/gen)</p></td>
<td><p>4.83e-9</p></td>
<td><p>Mutation rate</p></td>
</tr>
</tbody>
</table>
</section>
<img alt="_images/sec_catalog_anapla_models_mallardblackduck_2l19.png" src="_images/sec_catalog_anapla_models_mallardblackduck_2l19.png" />
</section>
</section>
<section id="sec_catalog_AnoCar">
<span id="sec_catalog_AnoCar"></span><h2>Anolis carolinensis<a class="headerlink" href="#sec_catalog_AnoCar" title="Permalink to this headline"></a></h2>
<dl class="field-list simple">
<dt class="field-odd">ID</dt>
<dd class="field-odd"><p>AnoCar</p>
</dd>
<dt class="field-even">Name</dt>
<dd class="field-even"><p>Anolis carolinensis</p>
</dd>
<dt class="field-odd">Common name</dt>
<dd class="field-odd"><p>Anole lizard</p>
</dd>
<dt class="field-even">Generation time</dt>
<dd class="field-even"><p>1.5 (<a class="reference external" href="https://doi.org/10.1093/ilar.45.1.54">Lovern et al., 2004</a>)</p>
</dd>
<dt class="field-odd">Population size</dt>
<dd class="field-odd"><p>3050000.0 (<a class="reference external" href="https://doi.org/10.1093/gbe/evz110">Pombi et al., 2019</a>)</p>
</dd>
</dl>
<section id="sec_catalog_AnoCar_genome">
<h3>Genome<a class="headerlink" href="#sec_catalog_AnoCar_genome" title="Permalink to this headline"></a></h3>
<table class="docutils align-default">
<colgroup>
<col style="width: 25%" />
<col style="width: 25%" />
<col style="width: 25%" />
<col style="width: 25%" />
</colgroup>
<thead>
<tr class="row-odd"><th class="head"><p>ID</p></th>
<th class="head"><p>Length</p></th>
<th class="head"><p>Recombination rate</p></th>
<th class="head"><p>Mutation rate</p></th>
</tr>
</thead>
<tbody>
<tr class="row-even"><td><p>1</p></td>
<td><p>263920458</p></td>
<td><p>1e-08</p></td>
<td><p>2.1e-10</p></td>
</tr>
<tr class="row-odd"><td><p>2</p></td>
<td><p>199619895</p></td>
<td><p>1e-08</p></td>
<td><p>2.1e-10</p></td>
</tr>
<tr class="row-even"><td><p>3</p></td>
<td><p>204416410</p></td>
<td><p>1e-08</p></td>
<td><p>2.1e-10</p></td>
</tr>
<tr class="row-odd"><td><p>4</p></td>
<td><p>156502444</p></td>
<td><p>1e-08</p></td>
<td><p>2.1e-10</p></td>
</tr>
<tr class="row-even"><td><p>5</p></td>
<td><p>150641573</p></td>
<td><p>1e-08</p></td>
<td><p>2.1e-10</p></td>
</tr>
<tr class="row-odd"><td><p>6</p></td>
<td><p>80741955</p></td>
<td><p>1e-08</p></td>
<td><p>2.1e-10</p></td>
</tr>
<tr class="row-even"><td><p>LGa</p></td>
<td><p>7025928</p></td>
<td><p>1e-08</p></td>
<td><p>2.1e-10</p></td>
</tr>
<tr class="row-odd"><td><p>LGb</p></td>
<td><p>3271537</p></td>
<td><p>1e-08</p></td>
<td><p>2.1e-10</p></td>
</tr>
<tr class="row-even"><td><p>LGc</p></td>
<td><p>9478905</p></td>
<td><p>1e-08</p></td>
<td><p>2.1e-10</p></td>
</tr>
<tr class="row-odd"><td><p>LGd</p></td>
<td><p>1094478</p></td>
<td><p>1e-08</p></td>
<td><p>2.1e-10</p></td>
</tr>
<tr class="row-even"><td><p>LGf</p></td>
<td><p>4257874</p></td>
<td><p>1e-08</p></td>
<td><p>2.1e-10</p></td>
</tr>
<tr class="row-odd"><td><p>LGg</p></td>
<td><p>424765</p></td>
<td><p>1e-08</p></td>
<td><p>2.1e-10</p></td>
</tr>
<tr class="row-even"><td><p>LGh</p></td>
<td><p>248369</p></td>
<td><p>1e-08</p></td>
<td><p>2.1e-10</p></td>
</tr>
<tr class="row-odd"><td><p>MT</p></td>
<td><p>17223</p></td>
<td><p>0</p></td>
<td><p>2.1e-10</p></td>
</tr>
</tbody>
</table>
<p>Mutation and recombination rates are in units of per bp and per generation.</p>
</section>
</section>
<hr class="docutils" />
<section id="sec_catalog_AnoGam">
<span id="sec_catalog_AnoGam"></span><h2>Anopheles gambiae<a class="headerlink" href="#sec_catalog_AnoGam" title="Permalink to this headline"></a></h2>
<dl class="field-list simple">
<dt class="field-odd">ID</dt>
<dd class="field-odd"><p>AnoGam</p>
</dd>
<dt class="field-even">Name</dt>
<dd class="field-even"><p>Anopheles gambiae</p>
</dd>
<dt class="field-odd">Common name</dt>
<dd class="field-odd"><p>Anopheles gambiae</p>
</dd>
<dt class="field-even">Generation time</dt>
<dd class="field-even"><p>0.09090909090909091 (<a class="reference external" href="https://doi.org/10.1038/nature24995">Ag1000G Consortium, 2017</a>)</p>
</dd>
<dt class="field-odd">Population size</dt>
<dd class="field-odd"><p>1000000.0 (<a class="reference external" href="https://doi.org/10.1038/nature24995">Ag1000G Consortium, 2017</a>)</p>
</dd>
</dl>
<section id="sec_catalog_AnoGam_genome">
<h3>Genome<a class="headerlink" href="#sec_catalog_AnoGam_genome" title="Permalink to this headline"></a></h3>
<table class="docutils align-default">
<colgroup>
<col style="width: 25%" />
<col style="width: 25%" />
<col style="width: 25%" />
<col style="width: 25%" />
</colgroup>
<thead>
<tr class="row-odd"><th class="head"><p>ID</p></th>
<th class="head"><p>Length</p></th>
<th class="head"><p>Recombination rate</p></th>
<th class="head"><p>Mutation rate</p></th>
</tr>
</thead>
<tbody>
<tr class="row-even"><td><p>2L</p></td>
<td><p>49364325</p></td>
<td><p>1.3e-08</p></td>
<td><p>3.5e-09</p></td>
</tr>
<tr class="row-odd"><td><p>2R</p></td>
<td><p>61545105</p></td>
<td><p>1.3e-08</p></td>
<td><p>3.5e-09</p></td>
</tr>
<tr class="row-even"><td><p>3L</p></td>
<td><p>41963435</p></td>
<td><p>1.3e-08</p></td>
<td><p>3.5e-09</p></td>
</tr>
<tr class="row-odd"><td><p>3R</p></td>
<td><p>53200684</p></td>
<td><p>1.6e-08</p></td>
<td><p>3.5e-09</p></td>
</tr>
<tr class="row-even"><td><p>X</p></td>
<td><p>24393108</p></td>
<td><p>2.04e-08</p></td>
<td><p>3.5e-09</p></td>
</tr>
<tr class="row-odd"><td><p>Mt</p></td>
<td><p>15363</p></td>
<td><p>0</p></td>
<td><p>3.5e-09</p></td>
</tr>
</tbody>
</table>
<p>Mutation and recombination rates are in units of per bp and per generation.</p>
</section>
<hr class="docutils" />
<section id="sec_catalog_AnoGam_models">
<h3>Demographic Models<a class="headerlink" href="#sec_catalog_AnoGam_models" title="Permalink to this headline"></a></h3>
<table class="docutils align-default">
<colgroup>
<col style="width: 50%" />
<col style="width: 50%" />
</colgroup>
<thead>
<tr class="row-odd"><th class="head"><p>ID</p></th>
<th class="head"><p>Description</p></th>
</tr>
</thead>
<tbody>
<tr class="row-even"><td><p><a class="reference internal" href="#sec_catalog_anogam_models_gabonag1000g_1a17">GabonAg1000G_1A17</a></p></td>
<td><p>Stairwayplot estimates of N(t) for Gabon sample</p></td>
</tr>
</tbody>
</table>
<section id="sec_catalog_anogam_models_gabonag1000g_1a17">
<span id="sec_catalog_anogam_models_gabonag1000g_1a17"></span><h4>Stairwayplot estimates of N(t) for Gabon sample<a class="headerlink" href="#sec_catalog_anogam_models_gabonag1000g_1a17" title="Permalink to this headline"></a></h4>
<p>
These estimates were done as part of the Ag1000G 2017 Consortium paper.
Stairwayplot was run with the addition of a
misorientation parameter using SFS information from each population.
The model contains 110 distinct epochs, so only some summaries
are reported in the population table.
</p>
<p class="rubric">Details</p>
<dl class="field-list simple">
<dt class="field-odd">ID</dt>
<dd class="field-odd"><p>GabonAg1000G_1A17</p>
</dd>
<dt class="field-even">Description</dt>
<dd class="field-even"><p>Stairwayplot estimates of N(t) for Gabon sample</p>
</dd>
<dt class="field-odd">Num populations</dt>
<dd class="field-odd"><p>1</p>
</dd>
</dl>
<p class="rubric">Populations</p>
<table class="docutils align-default">
<colgroup>
<col style="width: 25%" />