ArticleScientific reports2014
Inferring phylogenies of evolving sequences without multiple sequence alignment.
Article in Scientific reports, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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Who cites it
32 citing papers in PubMed.
- Estimating Genome-Wide Phylogenies Using Probabilistic Topic Modeling.Systematic biology · 2025Article
- New groups of highly divergent proteins in families as old as cellular life with important biological functions in the ocean.Environmental microbiome · 2025Article
- Evolutionary responses of a reef-building coral to climate change at the end of the last glacial maximum.Molecular biology and evolution · 2022Article
- Alignment-Free Analysis of Whole-Genome Sequences From Symbiodiniaceae Reveals Different Phylogenetic Signals in Distinct Regions.Frontiers in plant science · 2022Article
- The Resolved Mutual Information Function as a Structural Fingerprint of Biomolecular Sequences for Interpretable Machine Learning Classifiers.Entropy (Basel, Switzerland) · 2021Article
- Accurate prediction of B-form/A-form DNA conformation propensity from primary sequence: A machine learning and free energy handshake.Patterns (New York, N.Y.) · 2021Article
- ToRQuEMaDA: tool for retrieving queried Eubacteria, metadata and dereplicating assemblies.PeerJ · 2021Article
- Comparative Genomics Supports That Brazilian BioethanolFrontiers in microbiology · 2021Article
- Inferring Phylogenomic Relationship of Microbes Using Scalable Alignment-Free Methods.Methods in molecular biology (Clifton, N.J.) · 2021Article
- The Nubeam reference-free approach to analyze metagenomic sequencing reads.Genome research · 2020Article
- Prostate cancer heterogeneity assessment with multi-regional sampling and alignment-free methods.NAR genomics and bioinformatics · 2020Article
- Article
- Codon Pairs are Phylogenetically Conserved: A comprehensive analysis of codon pairing conservation across the Tree of Life.PloS one · 2020Article
- Benchmarking of alignment-free sequence comparison methods.Genome biology · 2019Article
- Alignment-free inference of hierarchical and reticulate phylogenomic relationships.Briefings in bioinformatics · 2019Review
- Alignment-Free Sequence Analysis and Applications.Annual review of biomedical data science · 2018Article
- S-plot2: Rapid Visual and Statistical Analysis of Genomic Sequences.Evolutionary bioinformatics online · 2018Article
- Article
- Reconstructing evolutionary trees in parallel for massive sequences.BMC systems biology · 2017Article
- Alignment-free sequence comparison: benefits, applications, and tools.Genome biology · 2017Review
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Alignment-free methods, in which shared properties of sub-sequences (e.g. identity or match length) are extracted and used to compute a distance matrix, have recently been explored for phylogenetic inference. However, the scalability and robustness of these methods to key evolutionary processes remain to be investigated. Here, using simulated sequence sets of various sizes in both nucleotides and amino acids, we systematically assess the accuracy of phylogenetic inference using an alignment-free approach, based on D2 statistics, under different evolutionary scenarios. We find that compared to a multiple sequence alignment approach, D2 methods are more robust against among-site rate heterogeneity, compositional biases, genetic rearrangements and insertions/deletions, but are more sensitive to recent sequence divergence and sequence truncation. Across diverse empirical datasets, the alignment-free methods perform well for sequences sharing low divergence, at greater computation speed. Our findings provide strong evidence for the scalability and the potential use of alignment-free methods in large-scale phylogenomics.
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