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有效的算法用于模拟沿着家族遗传树的序列

Elya Wygoda¹, Asher Moshe¹, Nimrod Serok¹

¹The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 69978, Israel.

Bioinformatics (Oxford, England)

|December 29, 2025

概括

有效的序列模拟加速了分子进化研究. 新的算法优化了插入/删除 (indel) 事件的处理,使得进化模型能够更快地进行遗传学分析和参数推断.

科学领域:

计算生物学计算生物学
分子进化分子进化
生物信息学是一种生物信息学.

背景情况:

在家族遗传树上的序列模拟对于基准算法和推断进化模型至关重要.
大致贝叶斯计算 (ABC) 方法需要广泛的模拟数据来实现复杂的进化模型.
计算高效的序列模拟器对于推进分子进化研究至关重要.

研究的目的:

开发和研究用于模拟沿着家族遗传树的序列的快速算法.
通过优化插入和删除 (indel) 事件的处理来加快模拟过程.
将一个高效的模拟器集成到基于ABC的算法中,用于推断indel模型参数.

主要方法:

开发和评估数据结构,以有效地存储沿着家族遗传树沿线发生的事件.
将新型模拟算法的性能与天真方法进行了比较.
将高效的模拟器集成到一个近似贝叶斯计算 (ABC) 框架中.

主要成果:

对于indel事件的高效数据结构显著加快了沿着家族遗传树的序列模拟.
开发的模拟器显示了与天真方法相比的实质性速度改进.
集成模拟器成功地被应用到使用ABC的Chiroptera中研究indel动力学.

结论:

优化处理indel事件是加速植物遗传序列模拟的关键.
新的高效模拟器提高了计算密集型遗传学分析的可行性.
这项工作为推断indel模型参数和研究进化动态提供了有价值的工具.

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