Scientific Computing Group, Heidelberg Institute for Theoretical Studies, 69118 Heidelberg and Department of Informatics, Institute of Theoretical Informatics, Karlsruhe Institute of Technology, 76128 Karlsruhe, Germany.
Bioinformatics. 2014 May 1;30(9):1312-3. doi: 10.1093/bioinformatics/btu033. Epub 2014 Jan 21.
Phylogenies are increasingly used in all fields of medical and biological research. Moreover, because of the next-generation sequencing revolution, datasets used for conducting phylogenetic analyses grow at an unprecedented pace. RAxML (Randomized Axelerated Maximum Likelihood) is a popular program for phylogenetic analyses of large datasets under maximum likelihood. Since the last RAxML paper in 2006, it has been continuously maintained and extended to accommodate the increasingly growing input datasets and to serve the needs of the user community.
I present some of the most notable new features and extensions of RAxML, such as a substantial extension of substitution models and supported data types, the introduction of SSE3, AVX and AVX2 vector intrinsics, techniques for reducing the memory requirements of the code and a plethora of operations for conducting post-analyses on sets of trees. In addition, an up-to-date 50-page user manual covering all new RAxML options is available.
系统发育在医学和生物学研究的所有领域中的应用越来越多。此外，由于下一代测序技术的发展，用于进行系统发育分析的数据集以前所未有的速度增长。RAxML（随机加速最大似然法）是一种用于最大似然法分析大型数据集的流行程序。自 2006 年最后一篇关于 RAxML 的论文发表以来，它一直在不断维护和扩展，以适应不断增长的输入数据集，并满足用户社区的需求。
我介绍了 RAxML 的一些最显著的新特性和扩展，例如对替代模型和支持的数据类型的大量扩展，SSE3、AVX 和 AVX2 向量特性的引入，用于降低代码内存需求的技术以及大量用于对树集进行后分析的操作。此外，还提供了一个最新的 50 页用户手册，涵盖了所有新的 RAxML 选项。
