ArticleNucleic acids research2013
Co-phylog: an assembly-free phylogenomic approach for closely related organisms.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 65 papers.
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65 citing papers in PubMed.
- A k-mer-based estimator of the substitution rate between repetitive sequences.Algorithms for molecular biology : AMB · 2026Article
- BioSet2Vec: extraction of k-mer dictionaries from multiple sets of biological sequences via big data technologies.BMC bioinformatics · 2025Article
- Sequence similarity estimation by random subsequence sketching.bioRxiv : the preprint server for biology · 2025Article
- Computational approaches for identifying neuropeptides: A comprehensive review.Molecular therapy. Nucleic acids · 2025Review
- An alignment-free method for phylogeny estimation using maximum likelihood.BMC bioinformatics · 2025Article
- An alignment- and reference-free strategy usingMycology · 2025Article
- A k-mer-Based Estimator of the Substitution Rate Between Repetitive Sequences.Algorithms in bioinformatics : ... International Workshop, WABI ..., proceedings. WABI (Workshop) · 2025Article
- Skmer approach improves species discrimination in taxonomically problematic genusPlant diversity · 2024Article
- Kssdtree: an interactive Python package for phylogenetic analysis based on sketching technique.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
- Enhancing Taxonomic Categorization of DNA Sequences with Deep Learning: A Multi-Label Approach.Bioengineering (Basel, Switzerland) · 2023Article
- Reference-free phylogeny from sequencing data.BioData mining · 2023Article
- Highly contiguous genomes of human clinical isolates ofMicrobial genomics · 2023Article
- How to optimally sample a sequence for rapid analysis.Bioinformatics (Oxford, England) · 2023Article
- Dissection of Besnoitia besnoiti intermediate host life cycle stages: From morphology to gene expression.PLoS pathogens · 2022Article
- Quantifying the uncertainty of assembly-free genome-wide distance estimates and phylogenetic relationships using subsampling.Cell systems · 2022Article
- Insertions and deletions as phylogenetic signal in an alignment-free context.PLoS computational biology · 2022Article
- Deep Ancestral Introgression Shapes Evolutionary History of Dragonflies and Damselflies.Systematic biology · 2022Article
- Space-efficient representation of genomic k-mer count tables.Algorithms for molecular biology : AMB · 2022Article
- In-depth investigation of the point mutation pattern of HIV-1.Frontiers in cellular and infection microbiology · 2022Article
5 more citing papers are in PubMed but not listed here.
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2 authors.
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Abstract
With the advent of high-throughput sequencing technologies, the rapid generation and accumulation of large amounts of sequencing data pose an insurmountable demand for efficient algorithms for constructing whole-genome phylogenies. The existing phylogenomic methods all use assembled sequences, which are often not available owing to the difficulty of assembling short-reads; this obstructs phylogenetic investigations on species without a reference genome. In this report, we present co-phylog, an assembly-free phylogenomic approach that creates a 'micro-alignment' at each 'object' in the sequence using the 'context' of the object and calculates pairwise distances before reconstructing the phylogenetic tree based on those distances. We explored the parameters' usages and the optimal working range of co-phylog, assessed co-phylog using the simulated next-generation sequencing (NGS) data and the real NGS raw data. We also compared co-phylog method with traditional alignment and alignment-free methods and illustrated the advantages and limitations of co-phylog method. In conclusion, we demonstrated that co-phylog is efficient algorithm and that it delivers high resolution and accurate phylogenies using whole-genome unassembled sequencing data, especially in the case of closely related organisms, thereby significantly alleviating the computational burden in the genomic era.
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