Using PhyloSuite for molecular phylogeny and tree?based analyses

Phylogenetic analysis has entered the genomics (multilocus) era. For less experienced researchers, conquering large number of software programs required for a multilocus-based phylogenetic reconstruction can be somewhat daunting and time-consuming. PhyloSuite, with user-friendly GUI, was designed to make this process more accessible by integrating multiple needed multilocus single-gene phylogenies further streamlining whole process. In protocol, we aim explain how conduct each step pipeline tree-based analyses in PhyloSuite. We also present new version PhyloSuite (v1.2.3), wherein fixed some bugs, made optimizations, introduced functions, including analyses, such as signal-to-noise calculation, saturation analysis, spurious species identification, etc. The step-by-step protocol includes background information (i.e., what does), reasons why do step), operations it). This will help researchers quick-start their way through especially those interested conducting organelle-based analyses.