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

Manolo Gouy (1) , Eric Tannier (1, 2) , Nicolas Comte (3) , David Parsons (2)

1 LBBE - Laboratoire de Biométrie et Biologie Evolutive - UMR 5558
2 BEAGLE - Artificial Evolution and Computational Biology
3 MORPHEO - Capture and Analysis of Shapes in Motion

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.

Domaines: Bio-informatique [q-bio.QM]

Manolo Gouy, Eric Tannier, Nicolas Comte, David Parsons. Seaview Version 5: A Multiplatform Software for Multiple Sequence Alignment, Molecular Phylogenetic Analyses, and Tree Reconciliation. Multiple Sequence Alignment, 2231, Humana, pp.241-260, 2021, Methods in Molecular Biology, ⟨10.1007/978-1-0716-1036-7_15⟩. ⟨hal-03065564⟩