Using PhyloSuite for molecular phylogeny and tree‐based analyses
Chuan‐Yu Xiang,
Fangluan Gao,
Ivan Jakovlić,
Hong‐Peng Lei,
Ye Hu,
Hong Zhang,
Hong Zou,
Gui‐Tang Wang,
Dong Zhang
Affiliations
Chuan‐Yu Xiang
State Key Laboratory of Grassland Agro‐Ecosystems, and College of Ecology Lanzhou University Lanzhou China
Fangluan Gao
Institute of Plant Virology, Fujian Agriculture and Forestry University Fuzhou China
Ivan Jakovlić
State Key Laboratory of Grassland Agro‐Ecosystems, and College of Ecology Lanzhou University Lanzhou China
Hong‐Peng Lei
State Key Laboratory of Grassland Agro‐Ecosystems, and College of Ecology Lanzhou University Lanzhou China
Ye Hu
State Key Laboratory of Grassland Agro‐Ecosystems, and College of Ecology Lanzhou University Lanzhou China
Hong Zhang
State Key Laboratory of Grassland Agro‐Ecosystems, and College of Ecology Lanzhou University Lanzhou China
Hong Zou
Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences Wuhan China
Gui‐Tang Wang
Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences Wuhan China
Dong Zhang
State Key Laboratory of Grassland Agro‐Ecosystems, and College of Ecology Lanzhou University Lanzhou China
Abstract Phylogenetic analysis has entered the genomics (multilocus) era. For less experienced researchers, conquering the large number of software programs required for a multilocus‐based phylogenetic reconstruction can be somewhat daunting and time‐consuming. PhyloSuite, a software with a user‐friendly GUI, was designed to make this process more accessible by integrating multiple software programs needed for multilocus and single‐gene phylogenies and further streamlining the whole process. In this protocol, we aim to explain how to conduct each step of the phylogenetic pipeline and tree‐based analyses in PhyloSuite. We also present a new version of PhyloSuite (v1.2.3), wherein we fixed some bugs, made some optimizations, and introduced some new functions, including a number of tree‐based analyses, such as signal‐to‐noise calculation, saturation analysis, spurious species identification, and etc. The step‐by‐step protocol includes background information (i.e., what the step does), reasons (i.e., why do the step), and operations (i.e., how to do it). This protocol will help researchers quick‐start their way through the multilocus phylogenetic analysis, especially those interested in conducting organelle‐based analyses.
