title: Next-Generation Anchor Based Phylogeny (NexABP): constructing phylogeny from next-generation sequencing data.
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.
authors.affiliation: School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi.
authors.forename: Tanmoy
authors.initials: T
authors.lastname: Roychowdhury
authors.forename: Anchal
authors.initials: A
authors.lastname: Vishnoi
authors.forename: Alok
authors.initials: A
authors.lastname: Bhattacharya
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D004926:Escherichia coli / Q000145:classification / Q000235:genetics; D016678:Genome; D023281:Genomics / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D009169:Mycobacterium tuberculosis / Q000145:classification / Q000235:genetics; D010802:Phylogeny; D017422:Sequence Analysis, DNA; D014734:Vibrio cholerae / Q000145:classification / Q000235:genetics
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