W-IQ-TREE: a fast online phylogenetic tool for maximum likelihood analysis - PubMed (original) (raw)
. 2016 Jul 8;44(W1):W232-5.
doi: 10.1093/nar/gkw256. Epub 2016 Apr 15.
Affiliations
- PMID: 27084950
- PMCID: PMC4987875
- DOI: 10.1093/nar/gkw256
W-IQ-TREE: a fast online phylogenetic tool for maximum likelihood analysis
Jana Trifinopoulos et al. Nucleic Acids Res. 2016.
Abstract
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 partition models. 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.
© The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.
Figures
Figure 1.
Number of all W-IQ-TREE jobs per month irrespective of the IP-addresses submitted by external users and number of distinct users per month.
Figure 2.
Screenshot of an example result with W-IQ-TREE for a chordate data set.
Similar articles
- IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies.
Nguyen LT, Schmidt HA, von Haeseler A, Minh BQ. Nguyen LT, et al. Mol Biol Evol. 2015 Jan;32(1):268-74. doi: 10.1093/molbev/msu300. Epub 2014 Nov 3. Mol Biol Evol. 2015. PMID: 25371430 Free PMC article. - PhyloDraw: a phylogenetic tree drawing system.
Choi JH, Jung HY, Kim HS, Cho HG. Choi JH, et al. Bioinformatics. 2000 Nov;16(11):1056-8. doi: 10.1093/bioinformatics/16.11.1056. Bioinformatics. 2000. PMID: 11159323 - SeaView version 4: A multiplatform graphical user interface for sequence alignment and phylogenetic tree building.
Gouy M, Guindon S, Gascuel O. Gouy M, et al. Mol Biol Evol. 2010 Feb;27(2):221-4. doi: 10.1093/molbev/msp259. Epub 2009 Oct 23. Mol Biol Evol. 2010. PMID: 19854763 - ConSurf 2016: an improved methodology to estimate and visualize evolutionary conservation in macromolecules.
Ashkenazy H, Abadi S, Martz E, Chay O, Mayrose I, Pupko T, Ben-Tal N. Ashkenazy H, et al. Nucleic Acids Res. 2016 Jul 8;44(W1):W344-50. doi: 10.1093/nar/gkw408. Epub 2016 May 10. Nucleic Acids Res. 2016. PMID: 27166375 Free PMC article. - [A bird's eye view of the algorithms and software packages for reconstructing phylogenetic trees].
Zhang LN, Rong CH, He Y, Guan Q, He B, Zhu XW, Liu JN, Chen HJ. Zhang LN, et al. Dongwuxue Yanjiu. 2013 Dec;34(6):640-50. Dongwuxue Yanjiu. 2013. PMID: 24415699 Review. Chinese.
Cited by
- Insights into the virome of Hyalomma marginatum in the Danube Delta: a major vector of Crimean-Congo hemorrhagic fever virus in Eastern Europe.
Bratuleanu BE, Chretien D, Bigot T, Regnault B, Pérot P, Savuta G, Eloit M, Temmam S. Bratuleanu BE, et al. Parasit Vectors. 2024 Nov 22;17(1):482. doi: 10.1186/s13071-024-06557-2. Parasit Vectors. 2024. PMID: 39578881 Free PMC article. - The nearly complete mitochondrial genome of the door snail Euphaedusa aculus (Stylommatophora: Clausiliidae) and phylogenetic analysis.
Liang QC, Tao KX, Qiao DD, Wang P, Yin HF, Yang QQ. Liang QC, et al. Mitochondrial DNA B Resour. 2024 Nov 20;9(11):1581-1585. doi: 10.1080/23802359.2024.2427105. eCollection 2024. Mitochondrial DNA B Resour. 2024. PMID: 39575206 Free PMC article. - A DNA-based approach to infer species diversity of larvae and adults from the white grub genus Phyllophaga (Coleoptera: Scarabeidae).
Guzmán-Franco AW, Rivero-Borja M, Marín-Jarillo A, Tamayo-Mejía F, Guzmán-Santillán N, Guzmán-Santillán T. Guzmán-Franco AW, et al. Front Insect Sci. 2024 Nov 7;4:1465794. doi: 10.3389/finsc.2024.1465794. eCollection 2024. Front Insect Sci. 2024. PMID: 39574960 Free PMC article. - Haplotypic Distribution of SARS-CoV-2 Variants in Cases of Intradomiciliary Infection in the State of Rondônia, Western Amazon.
Teixeira KS, Custódio MGF, Sgorlon G, Roca TP, Queiroz JADS, Passos-Silva AM, Ribeiro J, Vieira D. Teixeira KS, et al. Bioinform Biol Insights. 2024 Nov 21;18:11779322241266354. doi: 10.1177/11779322241266354. eCollection 2024. Bioinform Biol Insights. 2024. PMID: 39574519 Free PMC article. - YeeE-like bacterial SoxT proteins mediate sulfur import for oxidation and signal transduction.
Li J, Göbel F, Hsu HY, Koch JN, Hager N, Flegler WA, Tanabe TS, Dahl C. Li J, et al. Commun Biol. 2024 Nov 21;7(1):1548. doi: 10.1038/s42003-024-07270-7. Commun Biol. 2024. PMID: 39572704 Free PMC article.
References
- Schmidt H.A., Strimmer K., Vingron M., von Haeseler A. TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics. 2002;18:502–504. - PubMed
- Guindon S., Dufayard J.F., Lefort V., Anisimova M., Hordijk W., Gascuel O. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst. Biol. 2010;59:307–321. - PubMed
- Lanfear R., Calcott B., Ho S.Y., Guindon S. Partitionfinder: combined selection of partitioning schemes and substitution models for phylogenetic analyses. Mol. Biol. Evol. 2012;29:1695–1701. - PubMed
Publication types
MeSH terms
Substances
LinkOut - more resources
Full Text Sources
Other Literature Sources