IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era

Abstract

Abstract IQ-TREE (http://www.iqtree.org, last accessed February 6, 2020) is a user-friendly and widely used software package for phylogenetic inference using maximum likelihood. Since the release of version 1 in 2014, we have continuously expanded IQ-TREE to integrate a plethora of new models of sequence evolution and efficient computational approaches of phylogenetic inference to deal with genomic data. Here, we describe notable features of IQ-TREE version 2 and highlight the key advantages over other software.

Keywords

Phylogenetic treeInferenceBiologyTree (set theory)Tree rearrangementSoftwareEvolutionary biologyComputational biologyPhylogenetic networkComputer scienceMachine learningArtificial intelligenceGeneticsGeneMathematicsProgramming language

MeSH Terms

EvolutionMolecularGenomicsModelsGeneticPhylogenySoftware

Affiliated Institutions

Related Publications

UFBoot2: Improving the Ultrafast Bootstrap Approximation

Diep Thi Hoang , Olga Chernomor , Arndt von Haeseler +2 more

The standard bootstrap (SBS), despite being computationally intensive, is widely used in maximum likelihood phylogenetic analyses. We recently proposed the ultrafast bootstrap a...

2017 Molecular Biology and Evolution 9740 citations

Terrace Aware Data Structure for Phylogenomic Inference from Supermatrices

Olga Chernomor , Arndt von Haeseler , Bùi Quang Minh

In phylogenomics the analysis of concatenated gene alignments, the so-called supermatrix, is commonly accompanied by the assumption of partition models. Under such models each g...

2016 Systematic Biology 2153 citations

TBtools: An Integrative Toolkit Developed for Interactive Analyses of Big Biological Data

Chengjie Chen , Hao Chen , Yi Zhang +4 more

The rapid development of high-throughput sequencing techniques has led biology into the big-data era. Data analyses using various bioinformatics tools rely on programming a...

2020 Molecular Plant 14052 citations

ePlant and the 3D Data Display Initiative: Integrative Systems Biology on the World Wide Web

Geoffrey Fucile , David Di Biase , Hardeep K. Nahal-Bose +7 more

Visualization tools for biological data are often limited in their ability to interactively integrate data at multiple scales. These computational tools are also typically limit...

2011 PLoS ONE 61 citations

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

Lam-Tung Nguyen , Heiko A. Schmidt , Arndt von Haeseler +1 more

Large phylogenomics data sets require fast tree inference methods, especially for maximum-likelihood (ML) phylogenies. Fast programs exist, but due to inherent heuristics to fin...

2014 Molecular Biology and Evolution 25080 citations

Publication Info

Year: 2020
Type: article
Volume: 37
Issue: 5
Pages: 1530-1534
Citations: 13807
Access: Closed

External Links

Download PDF (Free) View on DOI.org PubMed Semantic Scholar

Social Impact

Altmetric

IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era

PlumX Metrics

Social media, news, blog, policy document mentions

Citation Metrics

13807

OpenAlex

2580

Influential

12643

CrossRef

Cite This

APA Style

                            
                                
                                    Bùi Quang Minh, 
                                
                                    Heiko A. Schmidt, 
                                
                                    Olga Chernomor
                                
                                et al.
                            
                            (2020). 
                            IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era. 
                            Molecular Biology and Evolution
                            , 37
                            (5)
                            , 1530-1534.
                            https://doi.org/10.1093/molbev/msaa015
                        

Identifiers

DOI: 10.1093/molbev/msaa015
PMID: 32011700
PMCID: PMC7182206

Data Quality

Data completeness: 90%