IQ-TREE statistics

To access cutting-edge analytics on consensus tools, life science contexts and associated fields, you will need to subscribe to our premium service.

Subscribe
info

Citations per year

Citations chart
info

Popular tool citations

chevron_left Phylogenetic inference chevron_right
Popular tools chart
info

Tool usage distribution map

Tool usage distribution map
info

Associated diseases

Associated diseases

Protocols

To access compelling stats and trends, optimize your time and resources and pinpoint new correlations, you will need to subscribe to our premium service.

Subscribe

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 Some 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 C, C#, C++, PHP
License GNU General Public License version 2.0
Computer skills Basic
Version 1.7
Stability Beta
Maintained Yes
Wikipedia https://github.com/Cibiv/IQ-TREE/wiki

Subtools


  • ModelFinder
  • PoMo (Polymorphism-aware phylogenetic Model)
  • revPOMO

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

Subtools


  • ModelFinder
  • PoMo (Polymorphism-aware phylogenetic Model)
  • revPOMO

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

 (33)
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 v7.271. columns with more than 50% of gaps were removed. phylogenetic trees were computed with iq-tree (automatic mode) 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 (), using separate substitution models for pufl and pufm alignment parts (so-called partition models, ). optimal amino acid substitution models were determined to be lg+r7 (pufl part) […]

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

[…] -linsi). multiple sequence alignments were trimmed using trimal [] (version 1.4.rev15) (parameter: -automated1). phylogenetic trees were inferred using the maximum likelihood method implemented in iq-tree [] (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: 5874029
PMID: 29590215
DOI: 10.1371/journal.pone.0194487

[…] generated by mafft [] with the l-ins-i method and poorly aligned sites or gaps were automatically removed from the final datasets by trimal []. finally, maximum likelihood trees were inferred by iq-tree [] with ultrafast bootstrapping [] under substitution models selected by the model test tool implemented in iq-tree for each dataset., in cases where homologs were not detected due […]

2018
PMCID: 5874253
PMID: 29593263
DOI: 10.1038/s41426-018-0049-6

[…] discarded and the remaining 72 aligned samples were subjected to phylogenetic analysis (see genbank accession numbers—supplementary table ). a maximum likelihood (ml) tree was generated using the iq-tree software. models were calculated using the -m test function and branch support was tested using 1000 ultrafast bootstraps. the bootstrap consensus tree was visualized with help of figtree […]


To access a full list of citations, you will need to upgrade to our premium service.

IQ-TREE in publications

 (165)
PMCID: 5954228
PMID: 29764946
DOI: 10.1128/mBio.00636-18

[…] prepared similarly to those described above. finally, 527 phylogenetic trees were reconstructed using the maximum-likelihood analysis and the ultrabootstrap method and 1,000 replications with the iq-tree tool (55 of the 582 alignments were discarded due to having a length shorter than 50 aa)., the whole-genome-wide snps were identified using bwa (), samtools (), picard tools […]

PMCID: 5954217
PMID: 29764951
DOI: 10.1128/mBio.00770-18

[…] genes hisd, pure, suca, thra, aroc, dnan, and hemd were aligned using mafft v7.305b () with the l-ins-i algorithm. the maximum likelihood tree was reconstructed based on the alignment with iq-tree v1.6.1 (), using modelfinder () to identify the most appropriate model. one thousand bootstraps were drawn with the ultrafast bootstrap approximation (). the model with the best fit […]

PMCID: 5951914
PMID: 29760453
DOI: 10.1038/s41467-018-04374-7

[…] (a lg+gamma model) and a gene-based partition scheme (1237 partitions; each has its own model). the two ml trees produced by raxml were topologically identical and were also found by the program iq-tree version 1.5.1. branch support for each internode was evaluated with 100 rapid bootstrapping replicates using raxml. because running an analysis using the site-heterogeneous cat model […]

PMCID: 5946053
PMID: 29748409
DOI: 10.1128/genomeA.00403-18

[…] and a membrane-associated protein) was found to be fragmented by an in-frame stop codon, but it was not established when these apparent mutations arose. phylogenetic analyses performed by using iq-tree () on the concatenated nucleotide sequences of the second exon of the dna packaging terminase subunit 1 gene and the entire dna polymerase catalytic subunit gene showed the closest […]

PMCID: 5940233
PMID: 29738547
DOI: 10.1371/journal.pone.0196995

[…] 7 [] with the default options. these alignments were refined manually based on conserved domains. maximum likelihood-based phylogenetic analysis and bootstrap methods (mlb) were conducted using iq-tree [] with 1,000 ultrafast bootstrap replications. the evolutionary model was ‘lg + i + g4’ [], which was automatically selected by the model test option incorporated in iq-tree. finally, highly […]


To access a full list of publications, you will need to upgrade to our premium service.

IQ-TREE institution(s)
Department of Ecology and Evolution, Research School of Biology, Australian National University, Canberra, ACT, Australia; Department of Biology, Indiana University, Bloomington, Indiana, USA; Department of Computer Science, Indiana University, Bloomington, IN, USA
IQ-TREE funding source(s)
Supported by the Australian National University Futures grant.

IQ-TREE reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review IQ-TREE