ArticleMolecular biology and evolution2023
PhylteR: Efficient Identification of Outlier Sequences in Phylogenomic Datasets.
Article in Molecular biology and evolution, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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19 citing papers in PubMed.
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- Phlag: scalable detection of genomics regions with unexplained phylogenetic heterogeneity.Bioinformatics (Oxford, England) · 2026Article
- Empirical Validation of the Nearly Neutral Theory at Divergence and Population-Genomic Scales Using 144 Placental Mammal Genomes.Genome biology and evolution · 2026Article
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- EMPIRICAL VALIDATION OF THE NEARLY NEUTRAL THEORY AT DIVERGENCE AND POPULATION GENOMIC SCALE USING 144 PLACENTAL MAMMALS GENOMES.bioRxiv : the preprint server for biology · 2026Article
- MagnetotacticISME communications · 2026Article
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- PickMe: Sample Selection for Species Tree Reconstruction using Coalescent Weighted Quartets.Systematic biology · 2025Article
- aPhyloGeo: a Python application for correlating genetic and climatic conditions.Bioinformatics (Oxford, England) · 2025Article
- Paleobiome dynamics shaped a large Gondwanan plant radiation.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
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- Giant multicellular magnetotactic prokaryotes in marine sediments.The ISME journal · 2025Article
- Discovering Fragile Clades and Causal Sequences in Phylogenomics by Evolutionary Sparse Learning.Molecular biology and evolution · 2024Article
- Microbial Diversity and Open Questions about the Deep Tree of Life.Genome biology and evolution · 2024Article
- Research on Fault Detection by Flow Sequence for Industrial Internet of Things in Sewage Treatment Plant Case.Sensors (Basel, Switzerland) · 2024Article
- OrthoMaM v12: a database of curated single-copy ortholog alignments and trees to study mammalian evolutionary genomics.Nucleic acids research · 2024Article
- Forty Years of Inferential Methods in the Journals of the Society for Molecular Biology and Evolution.Molecular biology and evolution · 2024Article
- Principal Component Analysis in Space Forms.IEEE transactions on signal processing : a publication of the IEEE Signal Processing Society · 2024Article
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10 authors.
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Abstract
In phylogenomics, incongruences between gene trees, resulting from both artifactual and biological reasons, can decrease the signal-to-noise ratio and complicate species tree inference. The amount of data handled today in classical phylogenomic analyses precludes manual error detection and removal. However, a simple and efficient way to automate the identification of outliers from a collection of gene trees is still missing. Here, we present PhylteR, a method that allows rapid and accurate detection of outlier sequences in phylogenomic datasets, i.e. species from individual gene trees that do not follow the general trend. PhylteR relies on DISTATIS, an extension of multidimensional scaling to 3 dimensions to compare multiple distance matrices at once. In PhylteR, these distance matrices extracted from individual gene phylogenies represent evolutionary distances between species according to each gene. On simulated datasets, we show that PhylteR identifies outliers with more sensitivity and precision than a comparable existing method. We also show that PhylteR is not sensitive to ILS-induced incongruences, which is a desirable feature. On a biological dataset of 14,463 genes for 53 species previously assembled for Carnivora phylogenomics, we show (i) that PhylteR identifies as outliers sequences that can be considered as such by other means, and (ii) that the removal of these sequences improves the concordance between the gene trees and the species tree. Thanks to the generation of numerous graphical outputs, PhylteR also allows for the rapid and easy visual characterization of the dataset at hand, thus aiding in the precise identification of errors. PhylteR is distributed as an R package on CRAN and as containerized versions (docker and singularity).
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