Phylogenetics

Is your phylogeny informative?

January 19, 2012 | Carl

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 ... [Read more...]

My talk on doing phylogenetics in R

November 18, 2011 | Scott Chamberlain

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 | cboettig

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 → [Read more...]

treebase package on cran

October 25, 2011 | Carl

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 ... [Read more...]

Showcasing the latest phylogenetic methods: AUTEUR

July 20, 2011 | Carl

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 ... [Read more...]

iEvoBio 2011 Synopsis

June 22, 2011 | Scott Chamberlain

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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TreeBASE in R: a first tutorial

May 16, 2011 | Carl

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 ... [Read more...]

Treebase trees from R

May 3, 2011 | Scott Chamberlain

Treebase is a great resource for phylogenetic trees, and has a nice interface for searching for certain types of trees. However, if you want to simply download a lot of trees for analyses (like that in Davies et al.), then you want to be able to access...
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Phylometa from R – UDPATE

April 1, 2011 | Scott Chamberlain

A while back I posted some messy code to run Phylometa from R, especially useful for processing the output data from Phylometa which is not easily done. The code is still quite messy, but it should work now. I have run the code with tens of different d...
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