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[ 源代码: seaview  ]

软件包:seaview(1:5.0.4-1)

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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.

标签: 领域: 生物学, 生物信息学, 实做语言: implemented-in::c, implemented-in::c++, 用户接口: 命令行, interface::graphical, interface::x11, 网络: 客户端, 网络协议: 需要一个额外的标签, 角色: role::program, scope::utility, 界面工具箱: FLTK, Purpose: 需要一个额外的标签, use::comparing, use::editing, 打印, use::viewing, works-with-format::plaintext, 处理: works-with::biological-sequence, x11::application

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