SNPGenie: estimating evolutionary parameters to detect natural selection using pooled next-generation sequencing data.

ABSTRACT:

Unlabelled

New applications of next-generation sequencing technologies use pools of DNA from multiple individuals to estimate population genetic parameters. However, no publicly available tools exist to analyse single-nucleotide polymorphism (SNP) calling results directly for evolutionary parameters important in detecting natural selection, including nucleotide diversity and gene diversity. We have developed SNPGenie to fill this gap. The user submits a FASTA reference sequence(s), a Gene Transfer Format (.GTF) file with CDS information and a SNP report(s) in an increasing selection of formats. The program estimates nucleotide diversity, distance from the reference and gene diversity. Sites are flagged for multiple overlapping reading frames, and are categorized by polymorphism typ

SUBMITTER: Nelson CW 

PROVIDER: S-EPMC4757956 | biostudies-literature | 2015 Nov

REPOSITORIES: biostudies-literature