geiger v2.0：一套用于将宏观进化模型拟合到系统发育树上的扩展方法。
geiger v2.0: an expanded suite of methods for fitting macroevolutionary models to phylogenetic trees.
机构信息
Department of Biological Sciences and Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID 83844, Department of Paleobiology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013, Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA, Department of Biological Sciences, Macquarie University, Sydney, NSW 2109, Australia and Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA.
Department of Biological Sciences and Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID 83844, Department of Paleobiology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013, Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA, Department of Biological Sciences, Macquarie University, Sydney, NSW 2109, Australia and Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA 90095, USADepartment of Biological Sciences and Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID 83844, Department of Paleobiology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013, Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA, Department of Biological Sciences, Macquarie University, Sydney, NSW 2109, Australia and Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA.
出版信息
Bioinformatics. 2014 Aug 1;30(15):2216-8. doi: 10.1093/bioinformatics/btu181. Epub 2014 Apr 10.
SUMMARY
Phylogenetic comparative methods are essential for addressing evolutionary hypotheses with interspecific data. The scale and scope of such data have increased dramatically in the past few years. Many existing approaches are either computationally infeasible or inappropriate for data of this size. To address both of these problems, we present geiger v2.0, a complete overhaul of the popular R package geiger. We have reimplemented existing methods with more efficient algorithms and have developed several new approaches for accomodating heterogeneous models and data types.
AVAILABILITY AND IMPLEMENTATION
This R package is available on the CRAN repository http://cran.r-project.org/web/packages/geiger/. All source code is also available on github http://github.com/mwpennell/geiger-v2. geiger v2.0 depends on the ape package.
CONTACT
SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
摘要
系统发育比较方法对于解决具有种间数据的进化假设至关重要。近年来，此类数据的规模和范围都有了显著的增长。许多现有的方法要么在计算上不可行，要么不适合这种规模的数据。为了解决这两个问题，我们提出了 geiger v2.0，这是流行的 R 包 geiger 的全面更新。我们使用更有效的算法重新实现了现有方法，并开发了几种新方法来适应异构模型和数据类型。
可用性和实现
这个 R 包可以在 CRAN 存储库 http://cran.r-project.org/web/packages/geiger/ 上找到。所有的源代码也可以在 github http://github.com/mwpennell/geiger-v2 上找到。geiger v2.0 依赖于 ape 包。
联系方式
补充信息
补充数据可在 Bioinformatics 在线获得。
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