IQ-TREE statistics

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Citations per year

Number of citations per year for the bioinformatics software tool IQ-TREE
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Tool usage distribution map

This map represents all the scientific publications referring to IQ-TREE per scientific context
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Associated diseases

This word cloud represents IQ-TREE usage per disease context
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Protocols

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


download.png

Versioning


No version available

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 citations

 (211)
library_books

Comparative Genomics Reveals the Core Gene Toolbox for the Fungus Insect Symbiosis

2018
MBio
PMCID: 5954228
PMID: 29764946
DOI: 10.1128/mBio.00636-18

[…] t in each fungal taxon was assessed using BLASTP. The enrichment heat map was produced using the “aheat map” function in R package “NMF” (). The cladogram of the included taxa was reconstructed using IQ-TREE, based on 29 proteins (longer than 50 aa) encoded by single-copy genes. The GO names and subcellular protein locations of the FISCoGs were predicted using Blast2GO v5.0 and the MultiLoc2 webse […]

call_split

Predictable Phenotypes of Antibiotic Resistance Mutations

2018
MBio
PMCID: 5954217
PMID: 29764951
DOI: 10.1128/mBio.00770-18
call_split See protocol

[…] rE, 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 was TIM+F+R3 (transition model [AC= […]

library_books

Evolutionary instability of CUG Leu in the genetic code of budding yeasts

2018
Nat Commun
PMCID: 5951914
PMID: 29760453
DOI: 10.1038/s41467-018-04374-7

[…] heme (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 in PhyloB […]

call_split

Genome Sequence of a Novel Alloherpesvirus Isolated from Glass Catfish (Kryptopterus bicirrhis)

2018
Genome Announc
PMCID: 5946053
PMID: 29748409
DOI: 10.1128/genomeA.00403-18
call_split See protocol

[…] tein, 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 relationshi […]

library_books

Plastid genome analysis of three Nemaliophycidae red algal species suggests environmental adaptation for iron limited habitats

2018
PLoS One
PMCID: 5940233
PMID: 29738547
DOI: 10.1371/journal.pone.0196995

[…] rsion 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 […]

library_books

Extensive gene rearrangements in the mitochondrial genomes of two egg parasitoids, Trichogramma japonicum and Trichogramma ostriniae (Hymenoptera: Chalcidoidea: Trichogrammatidae)

2018
Sci Rep
PMCID: 5935716
PMID: 29728615
DOI: 10.1038/s41598-018-25338-3

[…] e the best partition and substitution models. Four independent Markov chains were run for 10 million metropolis-coupled generations, with tree sampling every 1000 generations and a burn-in of 25%. In IQ-TREE analyses, the number of bootstrap replicates was set to 1000 with CAT model (C20 + 4 G). The CAT-GTR model was applied in PhyloBayes analyses with independent Markov chain runs of 8000 and a b […]


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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.

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