Gao Fangluan, Chen Chengjie, Arab Daej A, Du Zhenguo, He Yehua, Ho Simon Y W
Fujian Key Laboratory of Plant Virology, Institute of Plant Virology Fujian Agriculture and Forestry University Fuzhou China.
School of Life and Environmental Sciences University of Sydney Sydney New South Wales Australia.
Ecol Evol. 2019 Mar 1;9(7):3891-3898. doi: 10.1002/ece3.5015. eCollection 2019 Apr.
The genomic signatures of positive selection and evolutionary constraints can be detected by analyses of nucleotide sequences. One of the most widely used programs for this purpose is CodeML, part of the PAML package. Although a number of bioinformatics tools have been developed to facilitate the use of CodeML, these have various limitations. Here, we present a wrapper tool named EasyCodeML that provides a user-friendly graphical interface for using CodeML. EasyCodeML has a custom running mode in which parameters can be adjusted to meet different requirements. It also offers a preset running mode in which an evolutionary analysis pipeline and publication-quality tables can be exported by a single click. EasyCodeML allows visualized, interactive tree labelling, which greatly simplifies the use of the branch, branch-site, and clade models of selection. The program allows comparison of major codon-based models for analyses of selection. EasyCodeML is a stand-alone package that is supported in Windows, Mac, and Linux operating systems, and is freely available at https://github.com/BioEasy/EasyCodeML.
通过对核苷酸序列的分析，可以检测到正选择和进化限制的基因组特征。用于此目的的最广泛使用的程序之一是CodeML，它是PAML软件包的一部分。尽管已经开发了许多生物信息学工具来方便CodeML的使用，但这些工具存在各种局限性。在这里，我们展示了一个名为EasyCodeML的包装工具，它为使用CodeML提供了一个用户友好的图形界面。EasyCodeML具有自定义运行模式，其中可以调整参数以满足不同需求。它还提供了一个预设运行模式，通过单次点击即可导出进化分析管道和具有发表质量的表格。EasyCodeML允许可视化的交互式树标记，这极大地简化了选择的分支、分支位点和进化枝模型的使用。该程序允许比较用于选择分析的主要基于密码子的模型。EasyCodeML是一个独立的软件包，支持Windows、Mac和Linux操作系统，可在https://github.com/BioEasy/EasyCodeML上免费获取。
