ArticleBMC genomics2015
An assembly and alignment-free method of phylogeny reconstruction from next-generation sequencing data.
Article in BMC genomics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 90 papers.
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Who cites it
90 citing papers in PubMed.
- A k-mer-based estimator of the substitution rate between repetitive sequences.Algorithms for molecular biology : AMB · 2026Article
- DipSkmer: Reference-free population genomics with diploid genome skims.bioRxiv : the preprint server for biology · 2026Article
- ReSkmer: modeling repeats allows k-mer-based alignment-free methods to calculate population genomic distances.Genome biology · 2026Article
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- MELO-ED: learning locality-sensitive multi-embeddings for edit distance.bioRxiv : the preprint server for biology · 2025Article
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- Subgenome Partitioning and Polyploid Genome Evolution in the Loach Family Botiidae (Order Cypriniformes).Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Starship giant transposable elements cluster by host taxonomy using k-mer-based phylogenetics.G3 (Bethesda, Md.) · 2025Article
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- EvANI benchmarking workflow for evolutionary distance estimation.Briefings in bioinformatics · 2025Article
- Efficient and robust search of microbial genomes via phylogenetic compression.Nature methods · 2025Article
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- EvANI benchmarking workflow for evolutionary distance estimation.bioRxiv : the preprint server for biology · 2025Article
- A k-mer-Based Estimator of the Substitution Rate Between Repetitive Sequences.Algorithms in bioinformatics : ... International Workshop, WABI ..., proceedings. WABI (Workshop) · 2025Article
- An alignment- and reference-free strategy usingMycology · 2025Article
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- Kssdtree: an interactive Python package for phylogenetic analysis based on sketching technique.Bioinformatics (Oxford, England) · 2024Article
- MIKE: an ultrafast, assembly-, and alignment-free approach for phylogenetic tree construction.Bioinformatics (Oxford, England) · 2024Article
- dna2bit: high performance genomic distance estimation software for microbial genome analysis.Frontiers in microbiology · 2024Article
30 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundNext-generation sequencing technologies are rapidly generating whole-genome datasets for an increasing number of organisms. However, phylogenetic reconstruction of genomic data remains difficult because de novo assembly for non-model genomes and multi-genome alignment are challenging.
resultsTo greatly simplify the analysis, we present an Assembly and Alignment-Free (AAF) method ( https://sourceforge.net/projects/aaf-phylogeny ) that constructs phylogenies directly from unassembled genome sequence data, bypassing both genome assembly and alignment. Using mathematical calculations, models of sequence evolution, and simulated sequencing of published genomes, we address both evolutionary and sampling issues caused by direct reconstruction, including homoplasy, sequencing errors, and incomplete sequencing coverage. From these results, we calculate the statistical properties of the pairwise distances between genomes, allowing us to optimize parameter selection and perform bootstrapping. As a test case with real data, we successfully reconstructed the phylogeny of 12 mammals using raw sequencing reads. We also applied AAF to 21 tropical tree genome datasets with low coverage to demonstrate its effectiveness on non-model organisms.
conclusionOur AAF method opens up phylogenomics for species without an appropriate reference genome or high sequence coverage, and rapidly creates a phylogenetic framework for further analysis of genome structure and diversity among non-model organisms.
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