Making trees in the Jupyter notebook (part 1 - IToL)

Updated 13-August-2015, see below.

Let's extend the previous post by scraping the CAZy website for accession numbers from genes in the glycoside hydrolase 5 (GH5) family. Then we can build a phylogenetic tree from these sequences and visualize how well the EC activities correspond to the phylogeny.

Unfortunately the ...

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Using rvest to scrape the CAZy website

I have been looking for a nice excuse to play with rvest and since we're starting to work with "CAZYme" gene annotations in the Buckley lab, scraping the CAZy website seemed like a good fit. I'm starting simple and will build as I go. This post is just ...

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Evaluating 515F primers

Before we begin, I stumbled across this really great blog post from the Knight lab that you should definitely check out if you're interested in SSU rRNA gene primers. They have some experimental data up which is great to see.

Let's start by summarizing a few key findings ...

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