SeaView Version 4: A Multiplatform Graphical User Interface for Sequence Alignment and Phylogenetic Tree Building

被引:4680
作者
Gouy, Manolo [1 ]
Guindon, Stephane [2 ,3 ]
Gascuel, Olivier [2 ]
机构
[1] Univ Lyon 1, CNRS, UMR 5558, Lab Biometrie & Biol Evolut, F-69622 Villeurbanne, France
[2] Univ Montpellier 2, CNRS, UMR 5506, LIRMM, Montpellier, France
[3] Univ Auckland, Dept Stat, Auckland 1, New Zealand
关键词
SeaView; multiple sequence alignment; molecular phylogeny; PhyML; graphical user interface; ALGORITHM; ACCURATE; SOFTWARE; TOOLS; DNA;
D O I
10.1093/molbev/msp259
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
We present SeaView version 4, a multiplatform program designed to facilitate multiple alignment and phylogenetic tree building from molecular sequence data through the use of a graphical user interface. SeaView version 4 combines all the functions of the widely used programs SeaView (in its previous versions) and Phylo_win, and expands them by adding network access to sequence databases, alignment with arbitrary algorithm, maximum-likelihood tree building with PhyML, and display, printing, and copy-to-clipboard of rooted or unrooted, binary or multifurcating phylogenetic trees. In relation to the wide present offer of tools and algorithms for phylogenetic analyses, SeaView is especially useful for teaching and for occasional users of such software. SeaView is freely available at http://pbil.univ-lyon1.fr/software/seaview.
引用
收藏
页码:221 / 224
页数:4
相关论文
共 25 条
[1]   Approximate likelihood-ratio test for branches: A fast, accurate, and powerful alternative [J].
Anisimova, Maria ;
Gascuel, Olivier .
SYSTEMATIC BIOLOGY, 2006, 55 (04) :539-552
[2]  
[Anonymous], 1987, Molecular Evolutionary Genetics, DOI DOI 10.7312/NEI-92038
[3]   Phylogeny.fr: robust phylogenetic analysis for the non-specialist [J].
Dereeper, A. ;
Guignon, V. ;
Blanc, G. ;
Audic, S. ;
Buffet, S. ;
Chevenet, F. ;
Dufayard, J. -F. ;
Guindon, S. ;
Lefort, V. ;
Lescot, M. ;
Claverie, J. -M. ;
Gascuel, O. .
NUCLEIC ACIDS RESEARCH, 2008, 36 :W465-W469
[4]   ProbCons: Probabilistic consistency-based multiple sequence alignment [J].
Do, CB ;
Mahabhashyam, MSP ;
Brudno, M ;
Batzoglou, S .
GENOME RESEARCH, 2005, 15 (02) :330-340
[5]   MUSCLE: multiple sequence alignment with high accuracy and high throughput [J].
Edgar, RC .
NUCLEIC ACIDS RESEARCH, 2004, 32 (05) :1792-1797
[6]   MULTIPLE ALIGNED SEQUENCE EDITOR (MASE) [J].
FAULKNER, DV ;
JURKA, J .
TRENDS IN BIOCHEMICAL SCIENCES, 1988, 13 (08) :321-322
[7]  
FELSENSTEIN J, 1985, EVOLUTION, V39, P783, DOI 10.1111/j.1558-5646.1985.tb00420.x
[8]  
Felsenstein J, 1993, PHYLIP: Phylogeny inference package
[9]  
Galtier N, 1996, COMPUT APPL BIOSCI, V12, P543
[10]   BIONJ: An improved version of the NJ algorithm based on a simple model of sequence data [J].
Gascuel, O .
MOLECULAR BIOLOGY AND EVOLUTION, 1997, 14 (07) :685-695