Code for inferring ancestral word orders and word order change dynamics from present day language data.

The code is relatively modular, with the following major parts:

EthnoScrape: A Python script to scrape the Ethnologue website and record genetic classifications.

Requires Beautiful Soup, which it's up to you to install.

WALS2SQL: Python code that takes the WALS .csv data files and produces an SQLite database that has the information needed for the TreeBuilder code to build various classes of estimated phylogenetic trees.

TreeBuilder: Python code that uses the results of EthnoScrape and WALS2SQL to build pairwise distance matrices between languages. Neighbour Joining is then used to turn these matrices into trees, which are later used as samples in an MCMC analysis.

Requires:
	NINJA, a Java implementation of Neighbour Joining by Travis
	Wheeler (see http://nimbletwist.com/software/ninja/).
	
	Dendropy, a Python library for doing phylogenetic stuff (see
	http://pythonhosted.org/DendroPy/).

	Newick, a Python library for parsing Newick format tree files
	by Thomas Mailund (see
	http://www.daimi.au.dk/~mailund/newick.html).  This could
	probably be replaced with Dendropy to minimise dependencies.

All the above three projects are included in this repository for
convenience of distribution.  I believe this is done in compliance
with the licenses for NINJA and Dendropy.  Strictly speaking, I
shouldn't be doing this for Newick.  I'll either replace it with
Dendropy or get the author's blessing in the near future...

Inference: Performs MCMC inference over ancestral word orders and word order change dynamics, using the trees produced by TreeBuilder. All of the computational heavy lifting is done in C, with convenient Python scripts to handle basic logic.

The C code requires the GNU Scientific Library (GSL) to compile, which
it's up to you to install.

MatlabAnalysis: MATLAB code to do some basic post-processing of the results produced by Inference and produce pretty pictures. MATLAB is awful and I would love to replace this with Python stuff: Pandas, Matplotlib, etc.