Posts Tagged ‘ Phylogenetics ’

Is your phylogeny informative?

January 19, 2012
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Is your phylogeny informative?

Yesterday my paper   appeared in early view in Evolution (author’s preprint),1 so I’d like to take this chance to share the back-story and highlight my own view on some of our findings, and the associated package on CRAN.2 I didn’t set out to write this paper.  I set out to write a very different

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My talk on doing phylogenetics in R

November 18, 2011
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My talk on doing phylogenetics in R

I gave a talk today on doing very basic phylogenetics in R, including getting sequence data, aligning sequence data, plotting trees, doing trait evolution stuff, etc.Please comment if you have code for doing bayesian phylogenetic inference in R.  ...

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R-TreeBASE Tutorial

October 28, 2011
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R-TreeBASE Tutorial

My treebase package is now up on the CRAN repository. (Source code is up, the binaries should appear soon). Here’s a few introductory examples to illustrate some of the functionality of the package. Thanks in part to new data deposition … Continue reading →

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treebase package on cran

October 25, 2011
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treebase package on cran

My treebase package is now up on the CRAN repository. (Source code is up, the binaries should appear soon). Here’s a few introductory examples to illustrate some of the functionality of the package. Thanks in part to new data deposition requirements at journals such as Evolution, Am Nat, and Sys Bio, and data management plan

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Tenure track position in systematics at the University of Vermont

August 22, 2011
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Tenure track position in systematics at the University of Vermont

There is an awesome position opening up for an assistant professor in systematics at the University of Vermont. Below is the announcement, and see the original post at the Distributed Ecology blog. Why is this related to R? One can do a lot of systemat...

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Showcasing the latest phylogenetic methods: AUTEUR

July 20, 2011
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Showcasing the latest phylogenetic methods: AUTEUR

While high-speed fish feeding videos may be the signature of the lab, dig a bit deeper and you’ll find a wealth of comparative phylogenetic methods sneaking in.  It’s a natural union — expert functional morphology is the key to good comparative methods, just as phylogenies hold the key to untangling the evolutionary origins of that

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iEvoBio 2011 Synopsis

June 22, 2011
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iEvoBio 2011 Synopsis

We just wrapped up the 2011 iEvoBio meeting. It was awesome! If you didn't go this year or last year, definitely think about going next year.Here is a list of the cool projects that were discussed at the meeting (apologies if I left some out):Vistrails...

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searching ITIS and fetching Phylomatic trees

June 3, 2011
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searching ITIS and fetching Phylomatic trees

I am writing a set of functions to search ITIS for taxonomic information (more databases to come) and functions to fetch plant phylogenetic trees from Phylomatic. Code at github.Also, see the examples in the demos folder on the Github site above.

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A simple function for plotting phylogenies in ggplot2

May 17, 2011
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A simple function for plotting phylogenies in ggplot2

I wrote a simple function for plotting a phylogeny in ggplot2. However, it only handles a 3 species tree right now, as I haven't figured out how to generalize the approach to N species.Any ideas on how to improve this?

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TreeBASE in R: a first tutorial

May 16, 2011
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TreeBASE in R: a first tutorial

My TreeBASE R package is essentially functional now.  Here’s a quick tutorial on the kinds of things it can do.  Grab the treebase package here, install and load the library into R. TreeBASE provides two APIs to query the database, one which searches by the metadata associated with different publications (called OAI-PMH), and another which

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