SeaView - Multiplatform GUI for molecular phylogeny

Version 5.0.5

NEW: seaview performs reconcilation between gene and species trees using Treerecs version 1.2
NEW: bootstrap support optionally with the "Transfer Bootstrap Expectation" method
NEW: trimming-rule to shorten long sequence names in phylogenetic trees
NEW: 64-bit version for the MS Windows platform
NEW: multiple-tree windows
NEW: seaview uses PHYLIP v3.696 to compute parsimony trees
NEW: seaview can be run without GUI using a command line
NEW: seaview drives the PhyML v3.1 program to compute maximum likelihood phylogenetic trees.
NEW: seaview drives the Gblocks program to select blocks of conserved sites.

SeaView is a multiplatform, graphical user interface for multiple sequence alignment and molecular phylogeny.

• SeaView reads and writes various file formats (NEXUS, MSF, CLUSTAL, FASTA, PHYLIP, MASE, Newick) of DNA and protein sequences and of phylogenetic trees.
• SeaView drives programs muscle or Clustal Omega for multiple sequence alignment, and also allows to use any external alignment algorithm able to read and write FASTA-formatted files.
• Seaview drives the Gblocks program to select blocks of evolutionarily conserved sites.
• SeaView computes phylogenetic trees by
• parsimony, using PHYLIP's dnapars/protpars algorithm,
• distance, with NJ or BioNJ algorithms on a variety of evolutionary distances,
• maximum likelihood, driving program PhyML 3.1.
• Seaview can use the Transfer Bootstrap Expectation method to compute the bootstrap support of PhyML and distance trees.
• Seaview uses the Treerecs method to reconcile gene and species trees.
• SeaView prints and draws phylogenetic trees on screen, SVG, PDF or PostScript files.
• SeaView allows to download sequences from EMBL/GenBank/UniProt using the Internet.

Screen shots of the main alignment and tree windows. Dialog window to perform Maximum-Likelihood tree-building.
On-line help document.Old seaview version 3.2

Download SeaView

Note for MS Windows users: The downloaded file (seaview5.exe) is a self-extracting archive: open it, and it will create a folder called seaview5 on your computer. The window that appears when you open seaview5.exe allows you to choose where to place the seaview5 folder. This folder contains the seaview program, an example data file, a .html file, and 5 other programs (muscle, clustalo, phyml, Gblocks, treerecs) that seaview drives. This folder contains also seaview32bit.exe, a 32-bit version of the seaview program. If you run a 32-bit version of MS Windows (typically Windows XP), you can discard seaview.exe and use seaview32bit.exe.

Note for Linux/Unix users: The downloaded archives contain the seaview executable itself, an example data file, a .html file, and 5 other programs (muscle, clustalo, phyml, Gblocks, treerecs) that seaview drives. These 5 programs and the .html file can either be left in the same directory as seaview, or be put in any directory of your PATH.

Note for macOS users: Right after decompression of the .zip file, it can be necessary to ctrl-click the seaview icon and select "Open" in the appearing menu. Once this has been done, seaview can be opened normally by double-clicking its icon.

Reference

If you use SeaView in a published work, please cite the following reference:

Gouy M., Guindon S. & Gascuel O. (2010) SeaView version 4 : a multiplatform graphical user interface for sequence alignment and phylogenetic tree building. Molecular Biology and Evolution 27(2):221-224.

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