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David Winter

Evolution, computational biology and genomics

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Software

Overview

  • rentrez

    rentrez is an R package for the NCBI EUtils API. Using this API, rentrez allows users search for, find cross-references among and download records from each of NCBI's databases (including GenBank, Pubmed and dbSNP). rentrez is part of the ROpenSci project, and the source repository provides extensive documentation for the package.
  • accuMUlate

    accuMUlate is a c++ program for identifying de novo mutations from NGS data generated from mutation accumulation (MA) experiments. In contrast to existing heuristic methods of mutation detection, accuMUlate takes a probabilistic approach to calling mutations, building a model that matches the design of MA experiments. It also collects a suite of statistics on each putatively mutant site, allowing users to identify likely false positives and calculates a demoninator for mutation rate calculations.
  • rotl

    rotl is an R package that provides and interface to the NSF-funded Open Tree of Life database. This package was developed as part of a NESCent hackathon, with François Michonneau, Joseph Brown and I contributing the project.
  • mmod

    Population geneticists have traditionally used as statistic called Nei's Gst to measure divergence between populations. However, it has become clear that Gst does not have a simple relationship to divergence, especially for very highly polymorphic loci.

    A number of new statistics have been developed to account for this problem, mmod is a package that brings three of these measures; Hedricks (2005, 2011) G''st Jost's (2008) D and Meirman's (2005) φ'st to R, along with a function that calculates Nei's Gst using nearly unbiased estimators for Hs and Ht (the two key parameters from which most of these stats are calculated). All these functions work on `genind` objects from the package `adegenet` so data can be read in from standard `genepop` for `fstat` files