IQ-TREE pipeline

IQ-TREE specifications

Information


Unique identifier OMICS_11543
Name IQ-TREE
Alternative name W-IQ-TREE
Interface Web user interface
Restrictions to use None
Input data DNA, amino acids, codons, binary and morphological data.
Input format PHYLIP, FASTA, Nexus, Clustal, MSF
Output data A self-readable report file and a NEWICK tree file.
Output format NEWICK
Programming languages PHP
Computer skills Basic
Version 1.4.2
Stability Stable
Maintained Yes
Wikipedia https://github.com/Cibiv/IQ-TREE/wiki

Subtool


  • ModelFinder

Documentation


Maintainer


  • person_outline Bui Quang Minh <>

Additional information


ModelFinder, implemented in IQ-TREE, is available here: http://www.iqtree.org/ModelFinder/ https://github.com/Cibiv/IQ-TREE/

Information


Unique identifier OMICS_11543
Name IQ-TREE
Alternative name W-IQ-TREE
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format PHYLIP, FASTA, Nexus, Clustal, MSF
Operating system Unix/Linux, Mac OS, Windows
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.6
Stability Beta
Source code URL https://codeload.github.com/Cibiv/IQ-TREE/tar.gz/v1.6.beta4
Maintained Yes
Wikipedia https://github.com/Cibiv/IQ-TREE/wiki

Subtool


  • ModelFinder

Download


Versioning


Add your version

Documentation


Maintainer


  • person_outline Bui Quang Minh <>

Additional information


ModelFinder, implemented in IQ-TREE, is available here: http://www.iqtree.org/ModelFinder/ https://github.com/Cibiv/IQ-TREE/

Publications for IQ-TREE

IQ-TREE IN pipelines

 (18)
2018
PMCID: 5788922
PMID: 29379078
DOI: 10.1038/s41467-017-02660-4

[…] a p-value cut-off of 1 × 10−5, and a percent match cut-off of 80. sequences were aligned with mafft v7.27168. columns with more than 50% of gaps were removed. phylogenetic trees were computed with iq-tree (automatic mode)69 and drawn with itol (https://itol.embl.de/)., the beco method is available in the flexflux library (http://lipm-bioinfo.toulouse.inra.fr/flexflux/documentation.html#beco). […]

2018
PMCID: 5810265
PMID: 29472894
DOI: 10.3389/fmicb.2017.02679

[…] and 180 aa (pufm), respectively. pufl and pufm msas were concatenated to form a single puflm msa. a maximum likelihood (ml) phylogenetic tree was calculated from the puflm msa with the program iq-tree v1.4.4 (nguyen et al., 2014), using separate substitution models for pufl and pufm alignment parts (so-called partition models, chernomor et al., 2016). optimal amino acid substitution models […]

2018
PMCID: 5810265
PMID: 29472894
DOI: 10.3389/fmicb.2017.02679

[…] models as the original ml tree. branch support values were assigned onto the original ml tree as the number of times each branch in the original tree occurred in the set of bootstrap replicates (iq-tree option ‘-sup’)., the calculated phylogenetic tree was midpoint-rooted with the r package phangorn v2.0.4 (schliep, 2011). for tree visualization itol v3.4.3 was used (letunic and bork, 2016). […]

2018
PMCID: 5851275
PMID: 29534719
DOI: 10.1186/s12915-018-0500-0

[…] -linsi). multiple sequence alignments were trimmed using trimal [80] (version 1.4.rev15) (parameter: -automated1). phylogenetic trees were inferred using the maximum likelihood method implemented in iq-tree [81] (version 1.4.4) (parameters: --test -bb 1000). for each reconstruction, the best model was selected using the --test parameter and 1000 ultrafast-bootstraps were computed., regarding […]

2018
PMCID: 5897096
PMID: 29648535
DOI: 10.7554/eLife.33034.033

[…] et al., 2009). proteins with trimmed alignments < 150 amino acids in length were excluded. the topologies of the remaining proteins were inferred using maximum likelihood as implemented in iq-tree v1.5.4 (nguyen et al., 2015) using an empirically determined substitution model and rapid bootstrapping (1000 replications). the phylogenies were midpoint rooted and branches with local […]

IQ-TREE institution(s)
Center for Integrative Bioinformatics, Max F Perutz Laboratories, University of Vienna, Medical University of Vienna, Vienna, Austria; Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, Vienna, Austria
IQ-TREE funding source(s)
IQ-TREE was partially funded by the Austrian Science Fund - FWF (grants I 760-B17 from 2012-2015 and I 2508-B29 from 2016-2019) and the University of Vienna (Initiativkolleg I059-N from 2011-2014).

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