The DOI matches its Crossref record; 34 of the 34 references it cites were found in a registry or an index.
New Methods to Calculate Concordance Factors for Phylogenomic Datasets
Open accessPublished version of a preprint
Abstract
We implement two measures for quantifying genealogical concordance in phylogenomic data sets: the gene concordance factor (gCF) and the novel site concordance factor (sCF). For every branch of a reference tree, gCF is defined as the percentage of “decisive” gene trees containing that branch. This measure is already in wide usage, but here we introduce a package that calculates it while accounting for variable taxon coverage among gene trees. sCF is a new measure defined as the percentage of decisive sites supporting a branch in the reference tree. gCF and sCF complement classical measures of branch support in phylogenetics by providing a full description of underlying disagreement among loci and sites. An easy to use implementation and tutorial is freely available in the IQ-TREE software package (http://www.iqtree.org/doc/Concordance-Factor, last accessed May 13, 2020).
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CONFIDENCE LIMITS ON PHYLOGENIES: AN APPROACH USING THE BOOTSTRAP
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IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies
Nguyen, L.-T., Schmidt, H. A., von Haeseler, A., & Minh, B. Q. (2015) · Molecular Biology and Evolution · doi:10.1093/molbev/msu300 · Cited by 26,046
Self-citationIQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era
Minh, B. Q., Schmidt, H. A., Chernomor, O., Schrempf, D., Woodhams, M. D., von Haeseler, A., & Lanfear, R. (2020) · Molecular Biology and Evolution · doi:10.1093/molbev/msaa015 · Cited by 16,873
Self-citationUFBoot2: Improving the Ultrafast Bootstrap Approximation
Hoang, D. T., Chernomor, O., von Haeseler, A., Minh, B. Q., & Vinh, L. S. (2018) · Molecular Biology and Evolution · doi:10.1093/molbev/msx281 · Cited by 10,881
Self-citationUltrafast Approximation for Phylogenetic Bootstrap
Minh, B. Q., Nguyen, M. A. T., & von Haeseler, A. (2013) · Molecular Biology and Evolution · doi:10.1093/molbev/mst024 · Cited by 4,844
Self-citationPhylogenomics resolves the timing and pattern of insect evolution
Misof, B., Liu, S., Meusemann, K., Peters, R. S., Donath, A., Mayer, C., Frandsen, P. B., Ware, J., Flouri, T., Beutel, R. G., et al. (2014) · Science · doi:10.1126/science.1257570 · Cited by 2,694
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IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era
Minh, B. Q., Schmidt, H. A., Chernomor, O., Schrempf, D., Woodhams, M. D., von Haeseler, A., & Lanfear, R. (2020) · Molecular Biology and Evolution · doi:10.1093/molbev/msaa015 · Cited by 16,873
Self-citationPlastid phylogenomic insights into relationships of all flowering plant families
Li, H.-T., Luo, Y., Gan, L., Ma, P.-F., Gao, L.-M., Yang, J.-B., Cai, J., Gitzendanner, M. A., Fritsch, P. W., Zhang, T., et al. (2021) · BMC Biology · doi:10.1186/s12915-021-01166-2 · Cited by 259
Incongruence in the phylogenomics era
Steenwyk, J. L., Li, Y., Zhou, X., Shen, X.-X., & Rokas, A. (2023) · Nature Reviews Genetics · doi:10.1038/s41576-023-00620-x · Cited by 259
Increased fidelity of protein synthesis extends lifespan
Martinez-Miguel, V. E., Lujan, C., Espie--Caullet, T., Martinez-Martinez, D., Moore, S., Backes, C., Gonzalez, S., Galimov, E. R., Brown, A. E. X., Halic, M., et al. (2021) · Cell Metabolism · doi:10.1016/j.cmet.2021.08.017 · Cited by 137
Prolonged morphological expansion of spiny-rayed fishes following the end-Cretaceous
Ghezelayagh, A., Harrington, R. C., Burress, E. D., Campbell, M. A., Buckner, J. C., Chakrabarty, P., Glass, J. R., McCraney, W. T., Unmack, P. J., Thacker, C. E., et al. (2022) · Nature Ecology & Evolution · doi:10.1038/s41559-022-01801-3 · Cited by 127
Metadata
- Authors
- Minh, B. Q., Hahn, M. W., & Lanfear, R.
- Venue
- Molecular Biology and Evolution
- Publisher
- Oxford University Press (OUP)
- Published
- 2020-05-04
- Volume
- 37
- Issue
- 9
- Pages
- 2727-2733
- ISSN
- 0737-4038 (ISSN-L)
- 1537-1719
- OpenAlex
- W3021936614
- Cited by
- 708
- References
- 34
- FWCI
- 24.34
- Type
- journal article
- Language
- en
- Open access
- hybrid
- Funders
- National Science Foundation (DEB-1936187)
- Australian National University Futures
- Australian Research Council (No. DP200103151)
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