The DOI matches its Crossref record; 63 of the 63 references it cites were found in a registry or an index.
Fast Coalescent-Based Computation of Local Branch Support from Quartet Frequencies
Open accessAbstract
Species tree reconstruction is complicated by effects of incomplete lineage sorting, commonly modeled by the multi-species coalescent model (MSC). While there has been substantial progress in developing methods that estimate a species tree given a collection of gene trees, less attention has been paid to fast and accurate methods of quantifying support. In this article, we propose a fast algorithm to compute quartet-based support for each branch of a given species tree with regard to a given set of gene trees. We then show how the quartet support can be used in the context of the MSC to compute (1) the local posterior probability (PP) that the branch is in the species tree and (2) the length of the branch in coalescent units. We evaluate the precision and recall of the local PP on a wide set of simulated and biological datasets, and show that it has very high precision and improved recall compared with multi-locus bootstrapping. The estimated branch lengths are highly accurate when gene tree estimation error is low, but are underestimated when gene tree estimation error increases. Computation of both the branch length and local PP is implemented as new features in ASTRAL.
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Cited by
ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees
Zhang, C., Rabiee, M., Sayyari, E., & Mirarab, S. (2018) · BMC Bioinformatics · doi:10.1186/s12859-018-2129-y · Cited by 2,471
Self-citationOne thousand plant transcriptomes and the phylogenomics of green plants
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New Methods to Calculate Concordance Factors for Phylogenomic Datasets
Minh, B. Q., Hahn, M. W., & Lanfear, R. (2020) · Molecular Biology and Evolution · doi:10.1093/molbev/msaa106 · Cited by 708
Large-scale ruminant genome sequencing provides insights into their evolution and distinct traits
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Self-citationPhylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea
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Metadata
- Authors
- Sayyari, E., & Mirarab, S.
- Venue
- Molecular Biology and Evolution
- Publisher
- Oxford University Press (OUP)
- Published
- 2016-04-15
- Volume
- 33
- Issue
- 7
- Pages
- 1654-1668
- ISSN
- 0737-4038 (ISSN-L)
- 1537-1719
- OpenAlex
- W2277574918
- Cited by
- 869
- References
- 63
- FWCI
- 27.24
- Type
- journal article
- Language
- en
- Open access
- hybrid
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