ReviewBriefings in bioinformatics2019
Alignment-free inference of hierarchical and reticulate phylogenomic relationships.
Review in Briefings in bioinformatics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
42 citing papers in PubMed.
- Revisiting Algorithms, Tools, and Applications for Sequence and Phylogenetic Analyses in the NGS-Based Omics Era.Biochemical genetics · 2026Review
- Sequence based virus host prediction: a curated dataset and generalizable framework for training artificial intelligence to identify viruses of humans.Virus evolution · 2026Article
- Current state and future prospects of Horizontal Gene Transfer detection.NAR genomics and bioinformatics · 2025Review
- Genetic Transfer in Action: Uncovering DNA Flow in an Extremophilic Microbial Community.Environmental microbiology · 2025Article
- An alignment- and reference-free strategy usingMycology · 2025Article
- TreeWave: command line tool for alignment-free phylogeny reconstruction based on graphical representation of DNA sequences and genomic signal processing.BMC bioinformatics · 2024Article
- Article
- Machine learning-based approach KEVOLVE efficiently identifies SARS-CoV-2 variant-specific genomic signatures.PloS one · 2024Article
- CGRWDL: alignment-free phylogeny reconstruction method for viruses based on chaos game representation weighted by dynamical language model.Frontiers in microbiology · 2024Article
- How to optimally sample a sequence for rapid analysis.Bioinformatics (Oxford, England) · 2023Article
- Synonymous nucleotide changes drive papillomavirus evolution.Tumour virus research · 2022Review
- MGTdb: a web service and database for studying the global and local genomic epidemiology of bacterial pathogens.Database : the journal of biological databases and curation · 2022Article
- Mathematical Approach to Protein Sequence Comparison Based on Physiochemical Properties.ACS omega · 2022Article
- Interpreting alignment-free sequence comparison: what makes a score a good score?NAR genomics and bioinformatics · 2022Article
- Insertions and deletions as phylogenetic signal in an alignment-free context.PLoS computational biology · 2022Article
- Metagenomic Geolocation Using Read Signatures.Frontiers in genetics · 2022Article
- Alignment-Free Analysis of Whole-Genome Sequences From Symbiodiniaceae Reveals Different Phylogenetic Signals in Distinct Regions.Frontiers in plant science · 2022Article
- Comparative analysis of alignment-free genome clustering and whole genome alignment-based phylogenomic relationship of coronaviruses.PloS one · 2022Article
- Alignment-free sequence comparison for virus genomes based on location correlation coefficient.Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases · 2021Article
- The Pectobacterium pangenome, with a focus on Pectobacterium brasiliense, shows a robust core and extensive exchange of genes from a shared gene pool.BMC genomics · 2021Article
Corrections and comments
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We are amidst an ongoing flood of sequence data arising from the application of high-throughput technologies, and a concomitant fundamental revision in our understanding of how genomes evolve individually and within the biosphere. Workflows for phylogenomic inference must accommodate data that are not only much larger than before, but often more error prone and perhaps misassembled, or not assembled in the first place. Moreover, genomes of microbes, viruses and plasmids evolve not only by tree-like descent with modification but also by incorporating stretches of exogenous DNA. Thus, next-generation phylogenomics must address computational scalability while rethinking the nature of orthogroups, the alignment of multiple sequences and the inference and comparison of trees. New phylogenomic workflows have begun to take shape based on so-called alignment-free (AF) approaches. Here, we review the conceptual foundations of AF phylogenetics for the hierarchical (vertical) and reticulate (lateral) components of genome evolution, focusing on methods based on k-mers. We reflect on what seems to be successful, and on where further development is needed.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.