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物理煤模拟:用于网络多种类的芽模型的模拟器,包括基因流传承的新扩展
John Fogg1, Elizabeth S Allman2, Cécile Ané1,3
1Department of Statistics, University of Wisconsin - Madison, WI, 53706, USA.
Systematic biology
|May 31, 2023
概括
我们介绍了一种新的网络凝聚模型,用于模拟基因树在基因谱物种网络中的进化,并考虑相关的基因流传承. 这个工具有助于模拟研究和演化生物学中的推断方法.
科学领域:
- 进化生物学 进化生物学
- 计算生物学 计算生物学
- 人类遗传学 是一个学科.
背景情况:
- 遗传学物种网络模拟了复杂的进化历史,超出了简单的分叉树.
- 网络多种合并过程对于理解这些网络内的基因树分歧至关重要.
研究的目的:
- 引入一种新的网络凝聚模型,结合基因流动的相关遗传.
- 概括现有的网络凝聚模型 (独立和共同继承).
主要方法:
- 使用迪里克莱特过程开发了一种新的网络凝聚模型,具有相关的继承.
- 在 Julia 包 PhyloCoalSimulations 中实现基因树模拟.
- 使用PhyloNetworks进行物种网络操纵和Newick格式输入/输出.
主要成果:
- 该模型允许在网络化事件中对基因流的相关遗传.
- 模拟的基因树可以保存关于它们在物种网络中的嵌入信息.
- 该软件支持以代或凝聚单位输入,以Newick格式输出.
结论:
- 该PhyloCoalSimulations包提供了一个灵活的工具,用于模拟各种网络凝聚场景下的基因树进化.
- 这便于下游分析,例如模拟特定物种的过程和推进基于模拟的推理方法.
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