使用XRate开发和应用异构系统发育模型
Developing and applying heterogeneous phylogenetic models with XRate
摘要：
在系统发育树上对序列进化进行建模是计算生物学中的一项有用技术。特别强大的模型，考虑到序列进化的异质性，根据“语法”的编码基因的功能。然而，除了适度的模型复杂性之外，模型的手动编码变得过于劳动密集。我们通过一组案例研究展示了XRate（宏和Scheme扩展）新的内置模型原型设计功能。这些功能允许快速实现系统发育模型，这在以前是劳动密集型的。还讨论了XRate用于特定谱系模型、祖先序列重建和改进的注释输出的新功能。XRate灵活的模型规范功能和计算效率使其非常适合开发和原型化系统发育语法模型。XRate作为DART软件包的一部分提供：http://biowiki.org/DART。
英文摘要：
Modeling sequence evolution on phylogenetic trees is a useful technique in computational biology. Especially powerful are models which take account of the heterogeneous nature of sequence evolution according to the "grammar" of the encoded gene features. However, beyond a modest level of model complexity, manual coding of models becomes prohibitively labor-intensive. We demonstrate, via a set of case studies, the new built-in model-prototyping capabilities of XRate (macros and Scheme extensions). These features allow rapid implementation of phylogenetic models which would have previously been far more labor-intensive. XRate's new capabilities for lineage-specific models, ancestral sequence reconstruction, and improved annotation output are also discussed. XRate's flexible model-specification capabilities and computational efficiency make it well-suited to developing and prototyping phylogenetic grammar models. XRate is available as part of the DART software package: http://biowiki.org/DART .
机构、总结、中文摘要均由AI分析而来，可能存在错误，请以论文正文为准。
