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Seaview Version 5: A Multiplatform Software for Multiple Sequence Alignment, Molecular Phylogenetic Analyses, and Tree Reconciliation

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Multiple Sequence Alignment

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2231))

Abstract

We present Seaview version 5, a multiplatform program to perform multiple alignment and phylogenetic tree building from molecular sequence data. Seaview provides network access to sequence databases, alignment with arbitrary algorithm, parsimony, distance and maximum likelihood tree building with PhyML, and display, printing, and copy-to-clipboard or to SVG files of rooted or unrooted, binary or multifurcating phylogenetic trees. While Seaview is primarily a program providing a graphical user interface to guide the user into performing desired analyses, Seaview possesses also a command-line mode adequate for user-provided scripts. Seaview version 5 introduces the ability to reconcile a gene tree with a reference species tree and use this reconciliation to root and rearrange the gene tree. Seaview is freely available at http://doua.prabi.fr/software/seaview.

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Acknowledgments

We thank the authors of all software bundled with Seaview (Clustal, muscle, gblocks, PhyML, PHYLIP, Treerecs) for permission to use these fine products. We thank Frédéric Lemoine and Olivier Gascuel for contributing code for the “Transfer bootstrap.”

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Authors and Affiliations

  1. Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, Villeurbanne, France

    Manolo Gouy & Eric Tannier

  2. INRIA Grenoble-Rhône-Alpes, Montbonnot, France

    Eric Tannier, Nicolas Comte & David P. Parsons

Authors
  1. Manolo Gouy
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  2. Eric Tannier
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  3. Nicolas Comte
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  4. David P. Parsons
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Corresponding author

Correspondence to Manolo Gouy .

Editor information

Editors and Affiliations

  1. Research Institute for Microbial Disease, Osaka University, Osaka, Japan

    Kazutaka Katoh

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Gouy, M., Tannier, E., Comte, N., Parsons, D.P. (2021). Seaview Version 5: A Multiplatform Software for Multiple Sequence Alignment, Molecular Phylogenetic Analyses, and Tree Reconciliation. In: Katoh, K. (eds) Multiple Sequence Alignment. Methods in Molecular Biology, vol 2231. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1036-7_15

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  • DOI: https://doi.org/10.1007/978-1-0716-1036-7_15

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-1035-0

  • Online ISBN: 978-1-0716-1036-7

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