Getting ETE3 Running on a Mac

Unfortunately, ETE, Python framework for the analysis and visualization of (phylogenetic) trees, is not currently available to install through MacPorts. The recommended way to install ETE on a Mac is through Anaconda or a Miniconda setup. I confess I was not familiar with the conda open source package management system, and I had not heard of Miniconda. I like Anaconda quite a lot, and I like it even more now that I know it’s part of a larger open source ecosystem, and it may be that one day I will switch over to it, but, right now, I am fairly happy with my Macports setup and I would rather not break what’s working.

To get a better sense of what I need to do, I clicked on the Linux native installation directions, which skip conda:

Install dependencies: python-qt4, python-lxml, python-six and python-numpy

Those don’t look too bad. Python Six, a compatibility library for Python 2 and 3, is available as py34-six. Done. As for the rest: py34-pyqt4, py34-lxml, and, of course, py34-numpy are already installed. Done, again.

It looks like pip will work here, so after making sure I have py34-pip installed and making sure I run sudo port --select pip pip34 to set it, I can run:

sudo pip install ete3

If I run an IDLE session and import ete3, I get no error prompts. Yay! Time to make some spam.

Fairytale Phylogeny

There’s been a lot of excitement/discussion over recent work on the phylogenetic of fairytales. Most folklorists will be excited, I think, to learn how much it relies upon older forms of folklore scholarship. In particular, some of the original work done by Jamie Tehrani used a version of motifs. I have compiled a chronology of the relevant discussion below. It includes some of the coverage given both to the initial PLoS ONE publication as well as to the later collaboration with Sara Gra├ža da Silva published in the Royal Society Open Science series in the press. (A fuller version of this chronology to include not only important antecedent scholarship but also annotations is forthcoming.)


November 13: Jamshid Tehrani’s “The Phylogeny of Little Red Riding Hood” appears on PLoS ONE.

November 14: Science reports on “The Evolution of Little Red Riding Hood”.

December 4: Patrice Lajoye, Julien d’Huy, and Jean-Loic Le Quellec commented on Tehrani in New Comparative Mythology.

December 11: Jamshid Tehrani responds in New Comparative Mythology.

2014 and 2015 are quiet. (At least so far as I know. I will look into this further when I get a chance.)


January 20: da Silve and Tehrani’s “Comparative phylogenetic analyses uncover the ancient roots of Indo-European folktales” appears in the Royal Society’s Open Science. The Atlantic covers the story on the same day in “The Fairy Tales That Predate Christianity” as does the BBC. (How did this happen?)

January 21: a robust conversation begins over on LanguageHat.

January 22: William Pooley documents some of the difficulties glossed over by da Silva and Tehrani that leads, he argues, prematurely to their conclusion that tales are more related by history than by geography in “Fairytale Genetics.”

January 25: The LanguageLog offers its own analysis of the problems with da Silva and Tehrani’s assumptions.

UPDATE: For those coming here from the recent 2017 Facebook group post: please note that a follow-up to this article never got posted because I began working through the methods that lie behind Tehrani’s work and got sidetracked in trying to figure out which parts I liked and which ones I was less comfortable with. That noted, Tehrani himself was very kind and generous in correspondence, and I own him a follow-up. As I also owe a follow-up to d’Huy who very kindly sent me a bibliography and other links. This is a robust sub-field!