ArticleScientific reports2013
Next-Generation Anchor Based Phylogeny (NexABP): constructing phylogeny from next-generation sequencing data.
Article in Scientific reports, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- Phylogenetic double placement of mixed samples.Bioinformatics (Oxford, England) · 2020Article
- 'Multi-SpaM': a maximum-likelihood approach to phylogeny reconstruction using multiple spaced-word matches and quartet trees.NAR genomics and bioinformatics · 2020Article
- Skmer: assembly-free and alignment-free sample identification using genome skims.Genome biology · 2019Article
- Cnidaria: fast, reference-free clustering of raw and assembled genome and transcriptome NGS data.BMC bioinformatics · 2015Article
- Analysis of IS6110 insertion sites provide a glimpse into genome evolution of Mycobacterium tuberculosis.Scientific reports · 2015Article
- An assembly and alignment-free method of phylogeny reconstruction from next-generation sequencing data.BMC genomics · 2015Article
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3 authors.
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Abstract
Whole genome sequences are ideally suited for deriving evolutionary relationship among organisms. With the availability of Next Generation sequencing (NGS) datasets in an unprecedented scale, it will be highly desirable if phylogenetic analysis can be carried out using short read NGS data. We described here an anchor based approach NexABP for phylogenetic construction of closely related strains/isolates from NGS data. This approach can be used even in the absence of a fully assembled reference genome and works by reducing the complexity of the datasets without compromising results. NexABP was used for constructing phylogeny of different strains of some of the common pathogens, such as Mycobacterium tuberculosis, Vibrio cholera and Escherichia coli. In addition to classification into distinct lineages, NexABP could resolve inner branches and also allow statistical testing using bootstrap analysis. We believe that there are some clear advantages of using NexABP based phylogenetic analysis as compared to other methods.
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