ArticleBMC evolutionary biology2007
Whole genome molecular phylogeny of large dsDNA viruses using composition vector method.
Article in BMC evolutionary biology, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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Who cites it
41 citing papers in PubMed.
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- Alignment-free comparison of metagenomics sequences via approximate string matching.Bioinformatics advances · 2022Article
- The viral capsid as novel nanomaterials for drug delivery.Future science OA · 2021Review
- CVTree: A Parallel Alignment-free Phylogeny and Taxonomy Tool Based on Composition Vectors of Genomes.Genomics, proteomics & bioinformatics · 2021Article
- Genome-wideGene reports · 2021Article
- Genomic analysis of Poxviridae and exploring qualified gene sequences for phylogenetics.Computational and structural biotechnology journal · 2021Article
- A new graph-theoretic approach to determine the similarity of genome sequences based on nucleotide triplets.Genomics · 2020Article
- Whole-genome-based phylogeny of African swine fever virus.Veterinary world · 2020Article
- Machine learning based imputation techniques for estimating phylogenetic trees from incomplete distance matrices.BMC genomics · 2020Article
- Resolution of deep divergence of club fungi (phylum Basidiomycota).Synthetic and systems biotechnology · 2019Article
- Identification and Visualization of Functionally Important Domains and Residues in Herpes Simplex Virus Glycoprotein K(gK) Using a Combination of Phylogenetics and Protein Modeling.Scientific reports · 2019Article
- Identification of Multiple Replication Stages and Origins in the Nucleopolyhedrovirus ofViruses · 2019Article
- SENSE: Siamese neural network for sequence embedding and alignment-free comparison.Bioinformatics (Oxford, England) · 2019Article
- Alignment-free method for DNA sequence clustering using Fuzzy integral similarity.Scientific reports · 2019Article
- Theoretical Foundation of the RelTime Method for Estimating Divergence Times from Variable Evolutionary Rates.Molecular biology and evolution · 2018Article
- Article
- Neptune: a bioinformatics tool for rapid discovery of genomic variation in bacterial populations.Nucleic acids research · 2017Article
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundOne important mechanism by which large DNA viruses increase their genome size is the addition of modules acquired from other viruses, host genomes or gene duplications. Phylogenetic analysis of large DNA viruses, especially using methods based on alignment, is often difficult due to the presence of horizontal gene transfer events. The recent composition vector approach, not sensitive to such events, is applied here to reconstruct the phylogeny of 124 large DNA viruses.
resultsThe results are mostly consistent with the biologist's systematics with only a few outliers and can also provide some information for those unclassified viruses and cladistic relationships of several families.
conclusionWith composition vector approach we obtained the phylogenetic tree of large DNA viruses, which not only give results comparable to biologist's systematics but also provide a new way for recovering the phylogeny of viruses.
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