期刊
MOLECULAR ECOLOGY RESOURCES
卷 17, 期 1, 页码 19-26出版社
WILEY
DOI: 10.1111/1755-0998.12567
关键词
genetics; package; phylogenies; R; software
资金
- Medical Research Council Centre for Outbreak Analysis
- National Institute for Health Research - Health Protection Research Unit (NIHR HPRU) in Modelling Methodology at Imperial College London
- Public Health England (PHE)
- National Science Foundation [DEB 1350474]
- United States Department of Agriculture (USDA) Agricultural Research Service (ARS) [5358-22000-039-00D]
- USDA Animal and Plant Health Inspection Service
- USDA-ARS Floriculture Nursery Initiative
- Oregon Department of Agriculture/Oregon Association of Nurseries (ODA-OAN)
- USDA Forest Service Forest Health Monitoring Program
- Medical Research Council [MR/K010174/1B] Funding Source: researchfish
- National Institute for Health Research [HPRU-2012-10080] Funding Source: researchfish
Genetic sequences of multiple genes are becoming increasingly common for a wide range of organisms including viruses, bacteria and eukaryotes. While such data may sometimes be treated as a single locus, in practice, a number of biological and statistical phenomena can lead to phylogenetic incongruence. In such cases, different loci should, at least as a preliminary step, be examined and analysed separately. The R software has become a popular platform for phylogenetics, with several packages implementing distance-based, parsimony and likelihood-based phylogenetic reconstruction, and an even greater number of packages implementing phylogenetic comparative methods. Unfortunately, basic data structures and tools for analysing multiple genes have so far been lacking, thereby limiting potential for investigating phylogenetic incongruence. In this study, we introduce the new R package apex to fill this gap. apex implements new object classes, which extend existing standards for storing DNA and amino acid sequences, and provides a number of convenient tools for handling, visualizing and analysing these data. In this study, we introduce the main features of the package and illustrate its functionalities through the analysis of a simple data set.
作者
我是这篇论文的作者
点击您的名字以认领此论文并将其添加到您的个人资料中。
推荐
暂无数据