Balík: seaview (1:5.0.4-1)

[ Zdroj: 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.

Značky: Pole: Biológia, Bioinformatika, Implementované v: implemented-in::c, implemented-in::c++, User Interface: Príkazový riadok, interface::graphical, interface::x11, Networking: Klient, Network Protocol: Need an extra tag, Role: role::program, scope::utility, Sada nástrojov používateľského rozhrania: 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

Ostatné balíky súvisiace s balíkom seaview

• dep: libc6 (>= 2.29)

  knižnica GNU C - zdieľané knižnice
  tiež virtuálny balík poskytovaný balíkom libc6-udeb

• dep: libfltk-images1.3

  Fast Light Toolkit - podpora načítavania obrázkov

• dep: libfltk1.3 (>= 1.3.4)

  Fast Light Toolkit - hlavná zdieľaná knižnica

• dep: libgcc-s1 (>= 3.0)

  podporná knižnica GCC

• dep: libstdc++6 (>= 5.2)

  štandardná knižnica C++ GNU v3

• dep: zlib1g (>= 1:1.1.4)

  komprimačná knižnica - dynamická verzia

• 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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