Using PhyloSuite for molecular phylogeny and tree‐based analyses

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.

Abstract

A new release of PhyloSuite, capable of conducting tree‐based analyses. Detailed guidelines for each step of phylogenetic and tree‐based analyses, following the “What? Why? and How?” structure. This protocol will help beginners learn how to conduct multilocus phylogenetic analyses and help experienced scientists improve their efficiency.

Highlights

• A new release of PhyloSuite, capable of conducting tree‐based analyses.

• Detailed guidelines for each step of phylogenetic and tree‐based analyses, following the “What, Why, and How” structure.

• This protocol will help beginners learn how to conduct multilocus phylogenetic analyses and help experienced scientists improve their efficiency.