ArticleAlgorithms for molecular biology : AMB2020
Alignment- and reference-free phylogenomics with colored de Bruijn graphs.
Article in Algorithms for molecular biology : AMB, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- 2Pipe starts with a question: matching you with the correct pipeline for MAG reconstruction.mSystems · 2026Review
- SANS ambages: phylogenomics with abundance-filter, multi-threading, and bootstrapping on amino-acid or genomic sequences.BMC bioinformatics · 2025Article
- Metagenomics-Toolkit: the flexible and efficient cloud-based metagenomics workflow featuring machine learning-enabled resource allocation.NAR genomics and bioinformatics · 2025Article
- Article
- Compression algorithm for colored de Bruijn graphs.Algorithms for molecular biology : AMB · 2024Article
- Compression Algorithm for Colored de Bruijn Graphs.Algorithms in bioinformatics : ... International Workshop, WABI ..., proceedings. WABI (Workshop) · 2023Article
- Quantifying the uncertainty of assembly-free genome-wide distance estimates and phylogenetic relationships using subsampling.Cell systems · 2022Article
- Scalable, ultra-fast, and low-memory construction of compacted de Bruijn graphs with Cuttlefish 2.Genome biology · 2022Article
- Complete pan-plastome sequences enable high resolution phylogenetic classification of sugar beet and closely related crop wild relatives.BMC genomics · 2022Article
- SANS serif: alignment-free, whole-genome-based phylogenetic reconstruction.Bioinformatics (Oxford, England) · 2021Article
- Data structures based onGenome research · 2021Review
- Bifrost: highly parallel construction and indexing of colored and compacted de Bruijn graphs.Genome biology · 2020Article
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1 author.
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Abstract
backgroundThe increasing amount of available genome sequence data enables large-scale comparative studies. A common task is the inference of phylogenies-a challenging task if close reference sequences are not available, genome sequences are incompletely assembled, or the high number of genomes precludes multiple sequence alignment in reasonable time.
resultsWe present a new whole-genome based approach to infer phylogenies that is alignment- and reference-free. In contrast to other methods, it does not rely on pairwise comparisons to determine distances to infer edges in a tree. Instead, a colored de Bruijn graph is constructed, and information on common subsequences is extracted to infer phylogenetic splits.
conclusionsThe introduced new methodology for large-scale phylogenomics shows high potential. Application to different datasets confirms robustness of the approach. A comparison to other state-of-the-art whole-genome based methods indicates comparable or higher accuracy and efficiency.
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