Pyvolve: A Flexible Python Module for Simulating Sequences along Phylogenies
Pyvolve: A Flexible Python Module for Simulating Sequences along Phylogenies
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DOI：
10.1371/journal.pone.0139047
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发表时间：
2015-09-23
期刊：
影响因子：
3.7
通讯作者：
Wilke, Claus O.
中科院分区：
文献类型：
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作者：
Spielman, Stephanie J.;Wilke, Claus O.
我们介绍Pyvolve，一个灵活的Python模块，用于模拟遗传数据沿着使用连续时间马尔可夫模型的序列进化的遗传学。Pyvolve可以很容易地集成到Python生物信息学管道中，它可以根据核苷酸、氨基酸和密码子序列进化的大多数标准模型来模拟序列。所有模型参数都是完全可定制的。用户还可以指定自定义进化模型，以及自定义速率矩阵和/或状态。这种灵活性使Pyvolve成为一个方便的框架，不仅可以在各种条件下模拟序列，还可以开发和测试新的进化模型。Pyvolve是一个FreeBSD许可下的开源项目，可以从http://github.com/sjspielman/pyvolve下载它，沿着详细的用户手册和示例脚本。
We introduce Pyvolve, a flexible Python module for simulating genetic data along a phylogeny using continuous-time Markov models of sequence evolution. Easily incorporated into Python bioinformatics pipelines, Pyvolve can simulate sequences according to most standard models of nucleotide, amino-acid, and codon sequence evolution. All model parameters are fully customizable. Users can additionally specify custom evolutionary models, with custom rate matrices and/or states to evolve. This flexibility makes Pyvolve a convenient framework not only for simulating sequences under a wide variety of conditions, but also for developing and testing new evolutionary models. Pyvolve is an open-source project under a FreeBSD license, and it is available for download, along with a detailed user-manual and example scripts, from http://github.com/sjspielman/pyvolve.