Next-Generation Anchor Based Phylogeny (NexABP): Constructing phylogeny from Next-generation sequencing data View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2013-12

AUTHORS

Tanmoy Roychowdhury, Anchal Vishnoi, Alok Bhattacharya

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. More... »

PAGES

2634

Identifiers

URI

http://scigraph.springernature.com/pub.10.1038/srep02634

DOI

http://dx.doi.org/10.1038/srep02634

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1007990863

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/24022334


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