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Analyzing ddRADseq Data in SNAPP

GitHub Gist


Over the last year, as I’ve become increasingly comfortable with GitHub, I’ve naturally shifted all of my note writing to Markdown language. During the process, I’ve started frequently jotting down useful notes related to analysis, code, or scientific computing as “Gists” on GitHub. In contrast to most repositories, Gists are small snippets of code or notes and are posted at gist.github.com rather than github.com. To date, I have published 8 Gists on topics as broad as Pandoc, ∂a∂i, SNAPP, and Markdown.

Recently, I published an updated public version of an earlier Gist containing a broad description of steps for analyzing SNP (single nucleotide polymorphism) data from ddRADseq loci in the software program SNAPP (Bryant et al. 2012; implemented in BEAST v2.4++), to infer species trees with divergence times. The new Gist lists 8 steps for doing this, which take advantage of several available software programs, as well as my own shell scripts. In the spirit of open science, my motivation for writing this note was that, while people don’t necessarily need another full-blown, in-depth tutorial on this (e.g. they can read this one), I could provide a set of steps that I used to prepare and analyze SNP data in SNAPP for recent projects.

Here is a link to the Gist.

Here, I am sharing this Gist with you as a link:


Cheers, ~J