Package: seaview (1:5.0.5-2)

[ Source: seaview  ]

Multiplatform interface for sequence alignment and phylogeny

SeaView is a viewer and editor of multiple sequence alignments, i.e. DNA or protein sequences are positioned each in their own separate line, such that the nucleotide/amino acid at a particular position (column) is presumed to have the same biochemical property.

SeaView reads and writes various file formats (NEXUS, MSF, CLUSTAL, FASTA, PHYLIP, MASE, Newick) of DNA and protein sequences and of phylogenetic trees. Alignments can be manually edited. It drives the programs Muscle or Clustal Omega for multiple sequence alignment, and also allows one to use any external alignment algorithm able to read and write FASTA-formatted files. It computes phylogenetic trees by parsimony using PHYLIP's dnapars/protpars algorithm, by distance with NJ or BioNJ algorithms on a variety of evolutionary distances, or by maximum likelihood using the program PhyML 3.0.

SeaView draws phylogenetic trees on screen or PostScript files, and allows one to download sequences from EMBL/GenBank/UniProt using the Internet.

Tags: Field: Biology, Bioinformatics, Implemented in: implemented-in::c, implemented-in::c++, User Interface: Command Line, interface::graphical, interface::x11, Networking: Client, Network Protocol: Need an extra tag, Role: role::program, scope::utility, Interface Toolkit: FLTK, Purpose: Need an extra tag, use::comparing, use::editing, Printing, use::viewing, works-with-format::plaintext, Works with: works-with::biological-sequence, x11::application

Other Packages Related to seaview

• dep: libc6 (>= 2.34)

  GNU C Library: Shared libraries
  also a virtual package provided by libc6-udeb

• dep: libfltk-images1.3

  Fast Light Toolkit - image loading support

• dep: libfltk1.3 (>= 1.3.4)

  Fast Light Toolkit - main shared library

• dep: libgcc-s1 (>= 3.5)

  GCC support library

• dep: libstdc++6 (>= 5.2)

  GNU Standard C++ Library v3

• dep: zlib1g (>= 1:1.1.4)

  compression library - runtime

• rec: clustalo

  General-purpose multiple sequence alignment program for proteins

• rec: muscle

  Multiple alignment program of protein sequences

• rec: phyml

  Phylogenetic estimation using Maximum Likelihood

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Architecture	Package Size	Installed Size	Files
armel	318.5 kB	947.0 kB	[list of files]