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Taraka Rama edited this page Apr 11, 2017 · 2 revisions

About CyBayes

CyBayes was written with the intent to provide a simple tool for linguists that can produce decent phylogenies using Bayesian methods for:

  • Binary cognate data
  • Multistate cognate data
  • Multiple aligned data in International Phonetic Alphabet that can be generated from [LingPy] (https://github.com/lingpy)

Inspiration

CyBayes is inspired by [MrBayes] (http://mrbayes.sourceforge.net/) that works from commandline and can infer high quality trees from binary coded cognate sets for large datasets.

Requirements

Using a multi-threaded compiled Numpy and Scipy will be useful for handling multistate datasets. The procedure is as followed for Ubuntu:

  • Install libopenblas-dev using apt
  • Install Numpy using pip3 as pip3 install numpy
  • Install Scipy using pip3 as pip3 install scipy
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