teaspoon

Tools for Evolutionary Analysis of Serially-sampled POpulati ONs

A package for sequence analysis of serially-sampled populations, implementing methods based on Bhatt et al. (2010; 2011) and Raghwani et al. (2016). This codebase is under development and not currently stable; users wanting to run analyses should use the existing Adapt-a-Rate v1.0 distribution (see below) and/or email the author, jayna.raghwani 'at' zoo.ox.ac.uk

Development / roadmap

The project changelog, and roadmap for future goals, are detailed in CHANGELOG.md.

Adapt-a-Rate

This project descends from the Adapt-a-Rate codebase developed by Samir Bhatt and Oliver G. Pybus at the Department of Zoology, Oxford University. This program estimates the rate of adaptive fixation in a population from sequences sampled at different points in time. It uses a population genetic method that is based on the MacDonald-Kreitman test. See the publications below for details.

Citation:

• Raghwani J, Bhatt S, Pybus OG (2016) Faster Adaptation in Smaller Populations: Counterintuitive Evolution of HIV during Childhood Infection. PLoS Computational Biology 12(1): e1004694. DOI: e1004694.
• Bhatt S, Holmes EC, Pybus OG (2011) The genomic rate of molecular adaptation of the human influenza A virus. Molecular Biology & Evolution 28:2443-51. DOI: 10.1093/molbev/msr044
• Bhatt S, Katzourakis A, Pybus OG (2010) Detecting natural selection in RNA virus populations using sequence summary statistics. Infection Genetics & Evolution 10:421-30. DOI: 10.1016/j.meegid.2009.06.001

Usage

Basic usage info at Usage.md but a manual/readthedocs is forthcoming.