Todd Knutson

A shorter version of my question: How can you re-root a tree after imported using the `read.raxml()` function?

I think I have a partial solution. The recently updated R package ape ver 4.0 included a new option in their `root()` function: `edgelabel = TRUE`. If you have bootstrapping...

I'm sorry, but I was wrong about the `midpoint()` function in the phangorn R package. This function works great. By default, it uses the option `node.labels = "support"`, which is...

Hi Guangchuang, Thanks for the link to your discussion with Klaus. This discussion and your comment above clears things up for me. I think if I take a tree with...

Hi Michael, Thanks for this tip (it took me a long time to figure that out!). This is what I am doing now. I import the _bipartitions_ file from RAxML...

Has anyone been able to generate screenshots using a krona.html file with [percent-encoding](https://en.wikipedia.org/wiki/Percent-encoding)? This would be helpful, because it could potentially allow you to automate the screenshot of an Krona...

In my opinion, this is a major problem. The true functionality might be explained somewhere in the paper or elsewhere, but quickly looking at these graphs, I feel most people...

I transitioned to using a different package, called `ggupset`. I asked how to solve this problem on their GitHub issues page and the developer provided a nice reproducible example. This...

I am also having this problem.

I think something happened when the commits from April 16, 2018, or Aug 19, 2018 (bfbe67e2e8c5198ccf77892e381304f8bae96e10 29e165e31eb23c546c47db34e419fab500ad6970 b33a5ba5d1c4bbb00b07b9436a7fe8956dcc51e0 0791ac23c5f7d40af2769d396de4b7ed54e3e200) were applied to the master branch. I restarted a new R...