Phylemon 2.0: a suite of web-tools for molecular evolution, phylogenetics, phylogenomics and hypotheses testing

被引：177

作者：

Sanchez, Ruben ^{[1
]}

Serra, Francois ^{[1
]}

Tarraga, Joaquin ^{[2
,3
]}

Medina, Ignacio ^{[2
,3
]}

Carbonell, Jose ^{[2
,3
]}

Pulido, Luis ^{[2
,3
]}

de Maria, Alejandro ^{[2
,3
]}

Capella-Gutierrez, Salvador ^{[4
]}

Huerta-Cepas, Jaime ^{[4
]}

Gabaldon, Toni ^{[4
]}

Dopazo, Joaquin ^{[2
,3
]}

Dopazo, Hernan ^{[1
]}

机构：

[1] Ctr Invest Principe Felipe CIPF, Evolutionary Genom Lab, Bioinformat & Genom Dept, Valencia 46013, Spain

[2] Ctr Invest Principe Felipe CIPF, Funct Genom Lab Bioinformat, Valencia 46013, Spain

[3] Ctr Invest Principe Felipe CIPF, Genom Dept, Valencia 46013, Spain

[4] UPF, Comparat Genom Grp, Bioinformat & Genom Programme, Ctr Genom Regulat CRG, Barcelona 08003, Spain

来源：

NUCLEIC ACIDS RESEARCH | 2011年 / 39卷

关键词：

MULTIPLE SEQUENCE ALIGNMENT; MAXIMUM-LIKELIHOOD; MODELS; SELECTION; ACCURATE; RATES; TREE;

D O I：

10.1093/nar/gkr408

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：

Phylemon 2.0 is a new release of the suite of web tools for molecular evolution, phylogenetics, phylogenomics and hypotheses testing. It has been designed as a response to the increasing demand of molecular sequence analyses for experts and non-expert users. Phylemon 2.0 has several unique features that differentiates it from other similar web resources: (i) it offers an integrated environment that enables evolutionary analyses, format conversion, file storage and edition of results; (ii) it suggests further analyses, thereby guiding the users through the web server; and (iii) it allows users to design and save phylogenetic pipelines to be used over multiple genes (phylogenomics). Altogether, Phylemon 2.0 integrates a suite of 30 tools covering sequence alignment reconstruction and trimming; tree reconstruction, visualization and manipulation; and evolutionary hypotheses testing.

引用

页码：W470 / W474

页数：5

共 23 条

[1] ProtTest: selection of best-fit models of protein evolution [J].

Abascal, F ;

Zardoya, R ;

Posada, D .

BIOINFORMATICS, 2005, 21 (09) :2104-2105

[2] NEW LOOK AT STATISTICAL-MODEL IDENTIFICATION [J].

AKAIKE, H .

IEEE TRANSACTIONS ON AUTOMATIC CONTROL, 1974, AC19 (06) :716-723

[3] Approximate likelihood-ratio test for branches: A fast, accurate, and powerful alternative [J].

Anisimova, Maria ;

Gascuel, Olivier .

SYSTEMATIC BIOLOGY, 2006, 55 (04) :539-552

[4]

[Anonymous], 2004, Inferring phylogenies

[5] LAGAN and Multi-LAGAN: Efficient tools for large-scale multiple alignment of genomic DNA [J].

Brudno, M ;

Do, CB ;

Cooper, GM ;

Kim, MF ;

Davydov, E ;

Green, ED ;

Sidow, A ;

Batzoglou, S .

GENOME RESEARCH, 2003, 13 (04) :721-731

[6] trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses [J].

Capella-Gutierrez, Salvador ;

Silla-Martinez, Jose M. ;

Gabaldon, Toni .

BIOINFORMATICS, 2009, 25 (15) :1972-1973

[7] 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

[8] MUSCLE: multiple sequence alignment with high accuracy and high throughput [J].

Edgar, RC .

NUCLEIC ACIDS RESEARCH, 2004, 32 (05) :1792-1797

[9]

Felsenstein J., 2004, Phylip (phylogeny inference package) version 3.6

[10] A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood [J].

Guindon, S ;

Gascuel, O .

SYSTEMATIC BIOLOGY, 2003, 52 (05) :696-704

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