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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

[…] a corresponding to appropriate substitutional models, the best partition scheme, phylogenomic tree reconstruction, and ultrafast bootstrap analyses were all inferred and analyses conducted within the IQ-TREE v1.5.3 package (). In order to test whether the revealed integer-multiple pattern of genome sizes was due to interspecies hybridization, we estimated the phylogenetic relationship of the multi […]

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

[…] nd amino acid sequences of the 13 protein-coding genes. Nucleotide sequences were aligned by codon using MAFFT version 7.205. Phylogenetic relationships were reconstructed with MrBayes version 3.2.5, IQ-TREE web server and PhyloBayes-MPI. In MrBayes analyses, matrices were partitioned by codon position. Then, we used PartitionFinder version 1.1.1 to determine the best partition and substitution mo […]

Citations

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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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