ReviewPhilosophical transactions of the Royal Society of London. Series B, Biological sciences2022
Recent progress on methods for estimating and updating large phylogenies.
Review in Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- Bioinformatics of Combined Nuclear and Mitochondrial Phylogenomics to Define Key Nodes for the Classification of Coleoptera.Systematic biology · 2026Article
- Theoretical estimates on the expected number of mutations needed to reconstruct clonal lineage trees.Bioinformatics advances · 2026Article
- Testing Phylogenetic Placement Accuracy of DNA Barcode Sequences on a Fish Backbone Tree: Implications of Backbone Tree Completeness and Species Representation.Ecology and evolution · 2025Article
- Sparse Neighbor Joining: rapid phylogenetic inference using a sparse distance matrix.Bioinformatics (Oxford, England) · 2024Article
- Mottle: Accurate pairwise substitution distance at high divergence through the exploitation of short-read mappers and gradient descent.PloS one · 2024Article
- Genomic population structures of microbial pathogens.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2022Article
- EnteroBase: hierarchical clustering of 100 000s of bacterial genomes into species/subspecies and populations.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2022Article
- Target capture and genome skimming for plant diversity studies.Applications in plant sciencesArticle
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2 authors.
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Abstract
With the increased availability of sequence data and even of fully sequenced and assembled genomes, phylogeny estimation of very large trees (even of hundreds of thousands of sequences) is now a goal for some biologists. Yet, the construction of these phylogenies is a complex pipeline presenting analytical and computational challenges, especially when the number of sequences is very large. In the past few years, new methods have been developed that aim to enable highly accurate phylogeny estimations on these large datasets, including divide-and-conquer techniques for multiple sequence alignment and/or tree estimation, methods that can estimate species trees from multi-locus datasets while addressing heterogeneity due to biological processes (e.g. incomplete lineage sorting and gene duplication and loss), and methods to add sequences into large gene trees or species trees. Here we present some of these recent advances and discuss opportunities for future improvements. This article is part of a discussion meeting issue 'Genomic population structures of microbial pathogens'.
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