ArticleNAR genomics and bioinformatics2022
Pitfalls of the site-concordance factor (sCF) as measure of phylogenetic branch support.
Article in NAR genomics and bioinformatics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
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Who cites it
3 citing papers in PubMed.
- BROOQS: Spectral Methods Resolve Level-1 Hybridization Cycles without Tests of Symmetry.bioRxiv : the preprint server for biology · 2026Article
- Genomic Distortion of Jawed Vertebrate Phylogeny.bioRxiv : the preprint server for biology · 2026Article
- The Meaning and Measure of Concordance Factors in Phylogenomics.Molecular biology and evolution · 2024Review
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Authors and funding
3 authors.
Funding
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Abstract
Confidence measures of branch reliability play an important role in phylogenetics as these measures allow to identify trees or parts of a tree that are well supported by the data and thus adequate to serve as basis for evolutionary inference of biological systems. Unreliable branch relationships in phylogenetic analyses are of concern because of their potential to represent incorrect relationships of interest among more reliable branch relationships. The site-concordance factor implemented in the IQ-TREE package is a recently introduced heuristic solution to the problem of identifying unreliable branch relationships on the basis of quartets. We test the performance of the site-concordance measure with simple examples based on simulated data and designed to study its behaviour in branch support estimates related to different degrees of branch length heterogeneities among a ten sequence tree. Our results show that in particular in cases of relationships with heterogeneous branch lengths site-concordance measures may be misleading. We therefore argue that the maximum parsimony optimality criterion currently used by the site-concordance measure may sometimes be poorly suited to evaluate branch support and that the scores reported by the site-concordance factor should not be considered as reliable.
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Registered trials
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