Generating reasonable starting trees for complex phylogenetic analyses

phylogenetics
software-peer-review
community
r
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#1

Author: April Wright

"I never really thought I would write an R package. I use R pretty casually. Then, this year, I was invited to participate during the last week of the Analytical Paleobiology short course, an intensive month-long experience in quantitative paleontology. I was thrilled to be invited. But I got a slight sinking feeling in my stomach when I realized all the materials were in R.

And so I, a Pythonista, decided I would spend some of my maternity leave writing R packages to try to blend in with students who had spent the month living and breathing R."

In this post, April describes her treestartr package for generating reasonable starting trees for complex phylogenetic analyses.

“From the user side, treestartr has four main utilities: to add taxa to a tree at random, to add taxa to a tree by guessing at taxonomy, to add taxa by hand, or to add taxa via a spreadsheet. All of these facilitate different aspects of the research, and I’ll talk about each in the context of how my students are using them.”

Read the full post here: https://ropensci.org/blog/2018/12/11/treestartr/