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A Practical Guide to Phylogenetics for Nonexperts
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Seaview Version 5: A Multiplatform Software for Multiple Sequence Alignment, Molecular Phylogenetic Analyses, and

Manolo Gouy1, Eric Tannier2,3, Nicolas Comte3

  • 1Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, Villeurbanne, France. manolo.gouy@univ-lyon1.fr.

Methods in Molecular Biology (Clifton, N.J.)
|December 8, 2020
PubMed
Summary
This summary is machine-generated.

Seaview version 5 offers enhanced molecular sequence analysis, including multiple alignment and phylogenetic tree construction. New features enable gene tree reconciliation with species trees for improved evolutionary insights.

Keywords:
Graphical user interfaceMolecular phylogenyMultiple sequence alignmentPhylogenetic tree buildingTree reconciliation

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Molecular Evolution

Background:

  • Accurate multiple sequence alignment and phylogenetic tree construction are fundamental in molecular biology.
  • Existing software often lacks integrated tools for advanced phylogenetic analyses and tree manipulation.

Purpose of the Study:

  • To introduce Seaview version 5, a comprehensive software for molecular sequence analysis.
  • To enhance phylogenetic tree building capabilities with new reconciliation features.
  • To provide a user-friendly yet powerful tool for both graphical and command-line users.

Main Methods:

  • Utilizes arbitrary algorithms for multiple sequence alignment.
  • Integrates parsimony, distance, and maximum likelihood methods for phylogenetic tree construction via PhyML.
  • Implements a novel gene tree reconciliation method with a reference species tree.

Main Results:

  • Seaview version 5 facilitates network access to sequence databases.
  • The software supports diverse tree visualization and export options (rooted/unrooted, binary/multifurcating, SVG).
  • The new reconciliation feature allows for rooting and rearranging gene trees based on species evolution.

Conclusions:

  • Seaview version 5 is a versatile and powerful tool for molecular sequence alignment and phylogenetic analysis.
  • The integration of gene tree reconciliation advances the study of evolutionary relationships.
  • The software's availability and dual interface modes cater to a wide range of users in bioinformatics and evolutionary research.