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      PhyloSuite: An integrated and scalable desktop platform for streamlined molecular sequence data management and evolutionary phylogenetics studies

      1 , 2 , 3 , 4 , 1 , 4 , 1 , 1
      Molecular Ecology Resources
      Wiley

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          Abstract

          <p class="first" id="d6315160e128">Multigene and genomic data sets have become commonplace in the field of phylogenetics, but many existing tools are not designed for such data sets, which often makes the analysis time-consuming and tedious. Here, we present PhyloSuite, a (cross-platform, open-source, stand-alone Python graphical user interface) user-friendly workflow desktop platform dedicated to streamlining molecular sequence data management and evolutionary phylogenetics studies. It uses a plugin-based system that integrates several phylogenetic and bioinformatic tools, thereby streamlining the entire procedure, from data acquisition to phylogenetic tree annotation (in combination with iTOL). It has the following features: (a) point-and-click and drag-and-drop graphical user interface; (b) a workplace to manage and organize molecular sequence data and results of analyses; (c) GenBank entry extraction and comparative statistics; and (d) a phylogenetic workflow with batch processing capability, comprising sequence alignment (mafft and macse), alignment optimization (trimAl, HmmCleaner and Gblocks), data set concatenation, best partitioning scheme and best evolutionary model selection (PartitionFinder and modelfinder), and phylogenetic inference (MrBayes and iq-tree). PhyloSuite is designed for both beginners and experienced researchers, allowing the former to quick-start their way into phylogenetic analysis, and the latter to conduct, store and manage their work in a streamlined way, and spend more time investigating scientific questions instead of wasting it on transferring files from one software program to another. </p>

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          Author and article information

          Journal
          Molecular Ecology Resources
          Mol Ecol Resour
          Wiley
          1755-098X
          1755-0998
          December 13 2019
          January 2020
          November 06 2019
          January 2020
          : 20
          : 1
          : 348-355
          Affiliations
          [1 ]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
          [2 ]University of Chinese Academy of Sciences Beijing China
          [3 ]Institute of Plant Virology Fujian Agriculture and Forestry University Fuzhou Fujian China
          [4 ]Bio‐Transduction Lab Wuhan China
          Article
          10.1111/1755-0998.13096
          31599058
          c9c237f2-1632-42c6-ba7b-7cf32f1f3173
          © 2020

          http://onlinelibrary.wiley.com/termsAndConditions#vor

          http://doi.wiley.com/10.1002/tdm_license_1.1

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