UFBoot2: Improving the Ultrafast Bootstrap Approximation

doi:10.1093/molbev/msx281

. 2018 Feb 1;35(2):518-522.

doi: 10.1093/molbev/msx281.

UFBoot2: Improving the Ultrafast Bootstrap Approximation

Diep Thi Hoang¹, Olga Chernomor², Arndt von Haeseler^{2

3}, Bui Quang Minh², Le Sy Vinh¹

Affiliations

¹ Faculty of Information Technology, University of Engineering and Technology, Vietnam National University, Hanoi, Vietnam.
² Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna, Medical University Vienna, Vienna, Austria.
³ Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, Vienna, Austria.

PMID: 29077904
PMCID: PMC5850222
DOI: 10.1093/molbev/msx281

UFBoot2: Improving the Ultrafast Bootstrap Approximation

Diep Thi Hoang et al. Mol Biol Evol. 2018.

. 2018 Feb 1;35(2):518-522.

doi: 10.1093/molbev/msx281.

Authors

Diep Thi Hoang¹, Olga Chernomor², Arndt von Haeseler^{2

3}, Bui Quang Minh², Le Sy Vinh¹

Affiliations

¹ Faculty of Information Technology, University of Engineering and Technology, Vietnam National University, Hanoi, Vietnam.
² Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna, Medical University Vienna, Vienna, Austria.
³ Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, Vienna, Austria.

PMID: 29077904
PMCID: PMC5850222
DOI: 10.1093/molbev/msx281

Abstract

The standard bootstrap (SBS), despite being computationally intensive, is widely used in maximum likelihood phylogenetic analyses. We recently proposed the ultrafast bootstrap approximation (UFBoot) to reduce computing time while achieving more unbiased branch supports than SBS under mild model violations. UFBoot has been steadily adopted as an efficient alternative to SBS and other bootstrap approaches. Here, we present UFBoot2, which substantially accelerates UFBoot and reduces the risk of overestimating branch supports due to polytomies or severe model violations. Additionally, UFBoot2 provides suitable bootstrap resampling strategies for phylogenomic data. UFBoot2 is 778 times (median) faster than SBS and 8.4 times (median) faster than RAxML rapid bootstrap on tested data sets. UFBoot2 is implemented in the IQ-TREE software package version 1.6 and freely available at http://www.iqtree.org.

Keywords: maximum likelihood; model violation; phylogenetic inference; polytomies; ultrafast bootstrap.

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Figures

<sc>Fig</sc>. 1. — **Fig. 1.**
Accuracy of the standard bootstrap (SBS), RAxML rapid bootstrap (RBS), ultrafast bootstrap (UFBoot2) and UFBoot2 with correction (UFBoot2 + NNI) for (A) correctly specified models and (B) severely misspecified models. The y-axis depicts the percentage of all branches with support value $x$ (across all reconstructed trees) that occur in the true tree. Curves above the diagonal indicate underestimation of branch supports whereas curves below the diagonal indicate overestimation. For each point $(x, y)$ in the curve representing the accuracy of bootstrap method M, x is an inferred bootstrap value by method M whereas y measures the probability of branches assigned by M with support value x to be true branches, that is, occurring on the true tree. Specifically, let $X^{+}$ ( $X^{-}$ ) be the set of branches with support value $x$ in all trees and present (absent) in the true tree. The $y$ value is computed as the ratio between ${| X}^{+} |$ and $| X$ |, where $|X| = {| X}^{+} | + {| X}^{-} |$ .

<sc>Fig</sc>. 2. — **Fig. 2.**
Maximum-likelihood tree inferred under the edge-unlinked partition model. Numbers attached to the branches show the UFBoot2 bootstrap supports using MSA-site, gene, and gene-site resampling strategies (omitted when all three supports are 100%).

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References

1. Bouchenak-Khelladi Y, Salamin N, Savolainen V, Forest F, van der Bank M, Chase MW, Hodkinson TR.. 2008. Large multi-gene phylogenetic trees of the grasses (Poaceae): progress towards complete tribal and generic level sampling. Mol Phylogenet Evol. 472:488–505. - PubMed
1. Chernomor O, von Haeseler A, Minh BQ.. 2016. Terrace aware data structure for phylogenomic inference from supermatrices. Syst Biol. 656:997–1008.http://dx.doi.org/10.1093/sysbio/syw037 - DOI - PMC - PubMed
1. Dell’Ampio E, Meusemann K, Szucsich NU, Peters RS, Meyer B, Borner J, Petersen M, Aberer AJ, Stamatakis A, Walzl MG, et al.2014. Decisive data sets in phylogenomics: lessons from studies on the phylogenetic relationships of primarily wingless insects. Mol Biol Evol. 311:239–249. - PMC - PubMed
1. Efron B. 1979. Bootstrap methods: another look at the jackknife. Ann Stat. 71:1–26.http://dx.doi.org/10.1214/aos/1176344552 - DOI
1. Fabre P-H, Rodrigues A, Douzery EJP.. 2009. Patterns of macroevolution among Primates inferred from a supermatrix of mitochondrial and nuclear DNA. Mol Phylogenet Evol. 533:808–825.http://dx.doi.org/10.1016/j.ympev.2009.08.004 - DOI - PubMed

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[1] Bouchenak-Khelladi Y, Salamin N, Savolainen V, Forest F, van der Bank M, Chase MW, Hodkinson TR.. 2008. Large multi-gene phylogenetic trees of the grasses (Poaceae): progress towards complete tribal and generic level sampling. Mol Phylogenet Evol. 472:488–505. - PubMed

[2] Bouchenak-Khelladi Y, Salamin N, Savolainen V, Forest F, van der Bank M, Chase MW, Hodkinson TR.. 2008. Large multi-gene phylogenetic trees of the grasses (Poaceae): progress towards complete tribal and generic level sampling. Mol Phylogenet Evol. 472:488–505. - PubMed

[3] Chernomor O, von Haeseler A, Minh BQ.. 2016. Terrace aware data structure for phylogenomic inference from supermatrices. Syst Biol. 656:997–1008.http://dx.doi.org/10.1093/sysbio/syw037 - DOI - PMC - PubMed

[4] Chernomor O, von Haeseler A, Minh BQ.. 2016. Terrace aware data structure for phylogenomic inference from supermatrices. Syst Biol. 656:997–1008.http://dx.doi.org/10.1093/sysbio/syw037 - DOI - PMC - PubMed

[5] Dell’Ampio E, Meusemann K, Szucsich NU, Peters RS, Meyer B, Borner J, Petersen M, Aberer AJ, Stamatakis A, Walzl MG, et al.2014. Decisive data sets in phylogenomics: lessons from studies on the phylogenetic relationships of primarily wingless insects. Mol Biol Evol. 311:239–249. - PMC - PubMed

[6] Dell’Ampio E, Meusemann K, Szucsich NU, Peters RS, Meyer B, Borner J, Petersen M, Aberer AJ, Stamatakis A, Walzl MG, et al.2014. Decisive data sets in phylogenomics: lessons from studies on the phylogenetic relationships of primarily wingless insects. Mol Biol Evol. 311:239–249. - PMC - PubMed

[7] Efron B. 1979. Bootstrap methods: another look at the jackknife. Ann Stat. 71:1–26.http://dx.doi.org/10.1214/aos/1176344552 - DOI

[8] Efron B. 1979. Bootstrap methods: another look at the jackknife. Ann Stat. 71:1–26.http://dx.doi.org/10.1214/aos/1176344552 - DOI

[9] Fabre P-H, Rodrigues A, Douzery EJP.. 2009. Patterns of macroevolution among Primates inferred from a supermatrix of mitochondrial and nuclear DNA. Mol Phylogenet Evol. 533:808–825.http://dx.doi.org/10.1016/j.ympev.2009.08.004 - DOI - PubMed

[10] Fabre P-H, Rodrigues A, Douzery EJP.. 2009. Patterns of macroevolution among Primates inferred from a supermatrix of mitochondrial and nuclear DNA. Mol Phylogenet Evol. 533:808–825.http://dx.doi.org/10.1016/j.ympev.2009.08.004 - DOI - PubMed

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UFBoot2: Improving the Ultrafast Bootstrap Approximation

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UFBoot2: Improving the Ultrafast Bootstrap Approximation

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