• こちらの2013/01/15の記事でSimRareを用いたシミュレーション・解析手法比較の実習をやっている
  • SimRare(文献)ではどんなモデルを想定してバリエーションを生成しているのだろうか
  • こちらがSimRareのサイト
  • チュートリアルの"Generation of variant data(こちら)"を読んでみる
    • Forward-time シミュレーション(変異を起こさせて、組換え・遺伝的浮動(こちら)・選択(選択係数(こちら)指定)・人口動態、の具合で現在のバリエーションに至らしめる)
    • 上記の進化的シナリオは実行者が決める(シナリオの定番がないからだが…)
    • 人口動態は人口の増大・ボトルネック(こちら)を複数回入れられる
    • その他、実装上の工夫としては、レアバリアントのプールを作れて、シミュレーションのたびにやり直すわけではないこと
    • 原文
This module repeatedly evolves a population of gene-based sequences using forward-time simulation with mutation, natural selection and demography. At the end of each repeated simulation, variant sites information such as minor allele frequencies, selection coefficients, position information will be saved. Overall, running this module will create a variant haplotype data pool for a gene region based on any user-defined evolutionary scenario. This simulation module is featured by its capability of incorporating multi-stage population expansion/bottleneck model, handling multi-locus selection model of fitness and random or locus-specific selection coefficient to novel variant, and simplicity of creating gene-based variant data pool based on which individuals' genotype of multiple sample replicates can be easily assigned without performing time-consuming evolutionary simulations round after round again. Eventually running this module, it creates reusable variant data pool based on the user-defined evolutionary scenario.

By launching SimRare program the GUI of this module is activated after triggering 'Need generate rare variant data pool ? --> Click Here', which is shown on the SimRare main window. A snapshot of the interface is like:

This module is implemented in SimuPOP (Peng and Kimmel 2005), a general purpose forward-time individual-based population genetics simulation framework and adapts features from srv (Peng and Liu 2011), a program implemented in SimuPOP to simulate sequences of the human genome with rare variants.