W-IQ-TREE: a fast online phylogenetic tool for maximum likelihood analysis

被引：3619

作者：

Trifinopoulos, Jana ^{[1
]}

Lam-Tung Nguyen ^{[1
]}

von Haeseler, Arndt ^{[1
,2
]}

Minh, Bui Quang ^{[1
]}

机构：

[1] Med Univ Vienna, Ctr Integrat Bioinformat, Univ Vienna, Max F Perutz Labs, A-1030 Vienna, Austria

[2] Univ Vienna, Fac Comp Sci, Bioinformat & Computat Biol, A-1090 Vienna, Austria

来源：

NUCLEIC ACIDS RESEARCH | 2016年 / 44卷 / W1期

基金：

奥地利科学基金会;

关键词：

PROTEIN EVOLUTION; INFERENCE; SELECTION; MODELS; RATES; APPROXIMATION; BOOTSTRAP; SCHEMES; SITES;

D O I：

10.1093/nar/gkw256

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：

This article presents W-IQ-TREE, an intuitive and user-friendly web interface and server for IQ-TREE, an efficient phylogenetic software for maximum likelihood analysis. W-IQ-TREE supports multiple sequence types (DNA, protein, codon, binary and morphology) in common alignment formats and a wide range of evolutionary models including mixture and partitionmodels. W-IQ-TREE performs fast model selection, partition scheme finding, efficient tree reconstruction, ultrafast bootstrapping, branch tests, and tree topology tests. All computations are conducted on a dedicated computer cluster and the users receive the results via URL or email. W-IQ-TREE is available at http://iqtree.cibiv.univie.ac.at. It is free and open to all users and there is no login requirement.

引用

页码：W232 / W235

页数：4

共 25 条

[1] NEW LOOK AT STATISTICAL-MODEL IDENTIFICATION
AKAIKE, H
[J]. IEEE TRANSACTIONS ON AUTOMATIC CONTROL, 1974, AC19 (06) : 716 - 723
[2] T-REX: a web server for inferring, validating and visualizing phylogenetic trees and networks
Alix, Boc
Boubacar, Diallo Alpha
Vladimir, Makarenkov
[J]. NUCLEIC ACIDS RESEARCH, 2012, 40 (W1) : W573 - W579
[3] Survey of Branch Support Methods Demonstrates Accuracy, Power, and Robustness of Fast Likelihood-based Approximation Schemes
Anisimova, Maria
Gil, Manuel
Dufayard, Jean-Francois
Dessimoz, Christophe
Gascuel, Olivier
[J]. SYSTEMATIC BIOLOGY, 2011, 60 (05) : 685 - 699
[4] Ultrafast Approximation for Phylogenetic Bootstrap
Bui Quang Minh
Minh Anh Thi Nguyen
von Haeseler, Arndt
[J]. MOLECULAR BIOLOGY AND EVOLUTION, 2013, 30 (05) : 1188 - 1195
[5] Consequences of Common Topological Rearrangements for Partition Trees in Phylogenomic Inference
Chernomor, Olga
Bui Quang Minh
von Haeseler, Arndt
[J]. JOURNAL OF COMPUTATIONAL BIOLOGY, 2015, 22 (12) : 1129 - 1142
[6] jModelTest 2: more models, new heuristics and parallel computing
Darriba, Diego
Taboada, Guillermo L.
Doallo, Ramon
Posada, David
[J]. NATURE METHODS, 2012, 9 (08) : 772 - 772
[7] ProtTest 3: fast selection of best-fit models of protein evolution
Darriba, Diego
Taboada, Guillermo L.
Doallo, Ramon
Posada, David
[J]. BIOINFORMATICS, 2011, 27 (08) : 1164 - 1165
[8] FELSENSTEIN J, 1985, EVOLUTION, V39, P783, DOI 10.1111/j.1558-5646.1985.tb00420.x
[9] PHYML Online - a web server for fast maximum likelihood-based phylogenetic inference
Guindon, S
Lethiec, F
Duroux, P
Gascuel, O
[J]. NUCLEIC ACIDS RESEARCH, 2005, 33 : W557 - W559
[10] New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0
Guindon, Stephane
Dufayard, Jean-Francois
Lefort, Vincent
Anisimova, Maria
Hordijk, Wim
Gascuel, Olivier
[J]. SYSTEMATIC BIOLOGY, 2010, 59 (03) : 307 - 321

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