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

There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

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.

Related collections

Most cited references 23

Record: found
Abstract: found
Article: not found

BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data.

O. Gascuel (1997)

We propose an improved version of the neighbor-joining (NJ) algorithm of Saitou and Nei. This new algorithm, BIONJ, follows the same agglomerative scheme as NJ, which consists of iteratively picking a pair of taxa, creating a new mode which represents the cluster of these taxa, and reducing the distance matrix by replacing both taxa by this node. Moreover, BIONJ uses a simple first-order model of the variances and covariances of evolutionary distance estimates. This model is well adapted when these estimates are obtained from aligned sequences. At each step it permits the selection, from the class of admissible reductions, of the reduction which minimizes the variance of the new distance matrix. In this way, we obtain better estimates to choose the pair of taxa to be agglomerated during the next steps. Moreover, in comparison with NJ's estimates, these estimates become better and better as the algorithm proceeds. BIONJ retains the good properties of NJ--especially its low run time. Computer simulations have been performed with 12-taxon model trees to determine BIONJ's efficiency. When the substitution rates are low (maximum pairwise divergence approximately 0.1 substitutions per site) or when they are constant among lineages, BIONJ is only slightly better than NJ. When the substitution rates are higher and vary among lineages,BIONJ clearly has better topological accuracy. In the latter case, for the model trees and the conditions of evolution tested, the topological error reduction is on the average around 20%. With highly-varying-rate trees and with high substitution rates (maximum pairwise divergence approximately 1.0 substitutions per site), the error reduction may even rise above 50%, while the probability of finding the correct tree may be augmented by as much as 15%.

0 comments Cited 609 times – based on 0 reviews      Review now

Bookmark

Record: found
Abstract: found
Article: found

Is Open Access

ASTRAL: genome-scale coalescent-based species tree estimation

S. Mirarab, R. Reaz, Md. S. Bayzid … (2014)

Motivation: Species trees provide insight into basic biology, including the mechanisms of evolution and how it modifies biomolecular function and structure, biodiversity and co-evolution between genes and species. Yet, gene trees often differ from species trees, creating challenges to species tree estimation. One of the most frequent causes for conflicting topologies between gene trees and species trees is incomplete lineage sorting (ILS), which is modelled by the multi-species coalescent. While many methods have been developed to estimate species trees from multiple genes, some which have statistical guarantees under the multi-species coalescent model, existing methods are too computationally intensive for use with genome-scale analyses or have been shown to have poor accuracy under some realistic conditions. Results: We present ASTRAL, a fast method for estimating species trees from multiple genes. ASTRAL is statistically consistent, can run on datasets with thousands of genes and has outstanding accuracy—improving on MP-EST and the population tree from BUCKy, two statistically consistent leading coalescent-based methods. ASTRAL is often more accurate than concatenation using maximum likelihood, except when ILS levels are low or there are too few gene trees. Availability and implementation: ASTRAL is available in open source form at https://github.com/smirarab/ASTRAL/. Datasets studied in this article are available at http://www.cs.utexas.edu/users/phylo/datasets/astral. Contact: warnow@illinois.edu Supplementary information: Supplementary data are available at Bioinformatics online.

0 comments Cited 472 times – based on 0 reviews      Review now

Bookmark

Record: found
Abstract: found
Article: not found

Estimating the pattern of nucleotide substitution.

Z. Yang (1994)

Knowledge of the pattern of nucleotide substitution is important both to our understanding of molecular sequence evolution and to reliable estimation of phylogenetic relationships. The method of parsimony analysis, which has been used to estimate substitution patterns in real sequences, has serious drawbacks and leads to results difficult to interpret. In this paper a model-based maximum likelihood approach is proposed for estimating substitution patterns in real sequences. Nucleotide substitution is assumed to follow a homogeneous Markov process, and the general reversible process model (REV) and the unrestricted model without the reversibility assumption are used. These models are also applied to examine the adequacy of the model of Hasegawa et al. (J. Mol. Evol. 1985;22:160-174) (HKY85). Two data sets are analyzed. For the psi eta-globin pseudogenes of six primate species, the REV models fits the data much better than HKY85, while, for a segment of mtDNA sequences from nine primates, REV cannot provide a significantly better fit than HKY85 when rate variation over sites is taken into account in the models. It is concluded that the use of the REV model in phylogenetic analysis can be recommended, especially for large data sets or for sequences with extreme substitution patterns, while HKY85 may be expected to provide a good approximation. The use of the unrestricted model does not appear to be worthwhile.

0 comments Cited 210 times – based on 0 reviews      Review now

Bookmark

All references

Author and article information

Contributors

Emma Teeling: Role: Editor

Journal

Journal ID (nlm-ta): Mol Biol Evol

Journal ID (iso-abbrev): Mol. Biol. Evol

Journal ID (publisher-id): molbev

Title: Molecular Biology and Evolution

Publisher: Oxford University Press

ISSN (Print): 0737-4038

ISSN (Electronic): 1537-1719

Publication date (Print): May 2020

Publication date (Electronic): 03 February 2020

Publication date PMC-release: 03 February 2020

Volume: 37

Issue: 5

Pages: 1530-1534

Affiliations

[m1 ] Research School of Computer Science , Australian National University, Canberra, ACT, Australia

[m2 ] Department of Ecology and Evolution , Research School of Biology, Australian National University, Canberra, ACT, Australia

[m3 ] Center for Integrative Bioinformatics Vienna , Max Perutz Labs, University of Vienna and Medical University of Vienna, Vienna, Austria

[m4 ] Department of Biological Physics , Eötvös Lórand University, Budapest, Hungary

[m5 ] Discipline of Mathematics , University of Tasmania, Hobart, TAS, Australia

[m6 ] Bioinformatics and Computational Biology , Faculty of Computer Science, University of Vienna, Vienna, Austria

Author notes

[†]

Arndt von Haeseler and Robert Lanfear contributed equally to this work.

Corresponding author: E-mail: m.bui@ 123456anu.edu.au .

Author information

Bui Quang Minh http://orcid.org/0000-0002-5535-6560

Article

Publisher ID: msaa015

DOI: 10.1093/molbev/msaa015

PMC ID: 7182206

PubMed ID: 32011700

SO-VID: 7771d037-5bb1-4b70-87f8-b7d006aa1851

License:

This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

History

Page count

Pages: 5

Funding

Funded by: Austrian Science Fund, DOI 10.13039/501100002428;

Award ID: I-2805-B29

Funded by: Australian National University Futures Scheme;

Funded by: European Research Council, DOI 10.13039/100010663;

Funded by: European Union's Horizon 2020 research and innovation programme;

Award ID: 714774

Comments

Comment on this article

scite_

Cited by 3,072

See all cited by

Most referenced authors 1,052

See all reference authors

- Version 1
- Version 1

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

Read this article at

Abstract

Related collections

Higher order chromatin architecture

Most cited references 23

BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data.

ASTRAL: genome-scale coalescent-based species tree estimation

Estimating the pattern of nucleotide substitution.

Author and article information

Contributors

Journal

Affiliations

Author notes

Author information

Article

History

Page count

Funding

Categories

Comments

Comment on this article

Similar content 116

Cited by 3,072

Most referenced authors 1,052