## Making trees in the Jupyter notebook (part 2 - Bokeh)

This post will work with the tree and information we produced in the last post. This time we'll use a Python plotting library called Bokeh to visualize the tree.

IToL is a great tool but on the flexibility front it can't compete with charting libraries like Matplotlib, ggvis ...

## 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 ...

## 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 ...

## Melting your phyloseq object with dplyr/tidyr

If you're a microbial ecologist and you haven't used phyloseq, put away your vintage scarf and thick-rimmed glasses because you are not hip. phyloseq is the nexus of all that is good in the universe. In this post we'll look at one of the greatest phyloseq functions ...

## 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 ...

## Exploring 515F primer targets in archaeal and bacterial SSU rRNA genes

Microbial ecologists have long considered the 515F SSU rRNA gene PCR primer to be "universal." That is, the 515F primer is thought to amplify Eukarya, Archaea, and Bacteria. Indeed the target of the 515F primer is well conserved across each domain, however, the there are some differences in the primer ...

## Creating custom bibliography styles with bibulous

Although biblatex citation styles are highly customizable, I recently gave bibulous a try and I've found it's a fantastic tool. bibulous allows you to write simple and concise style templates. Let's give it a spin...

The ISMEJ citation style for articles looks like so:

Maymo-Gatell X, Chien ...