workflow.txt

Requirements:

- Python v.2.7
- Python packages:
  o biopython
  o ete2
  o igraph
  o Levenshtein
  o multiprocessing
  o numpy
  o pandas
  o re
  o scipy
  o sklearn
- R v. 3.0.2
- R packages:
  o ape
- Paup* (available from https://people.sc.fsu.edu/~dswofford/paup_test/)
- BayesTraits (available from http://www.evolution.rdg.ac.uk/BayesTraits.html)
- MrBayes (available from http://mrbayes.sourceforge.net/), compiled for MPI
- MPI
- treeannotator (available as part of BEAST v.2 from http://www.beast2.org/)


Workflow:
The entire workflow can be replicated by issuing the commands below in the order listed. 
The script estimatePMI.py requires 50 cores on a parallel Unix server, and the MrBayes
command requires 8 cores. Please adapt to your hardware.

> python estimatePMI.py
> python cognateClustering.py
> python combinePartitions.py
> mpirun -np 8 mb -i albanoRomance.mb.nex
> R --vanilla < convertTrees.r
> python mbPostprocessing.py
> treeannotator albanoRomance.posterior.tree albanoRomance.mcc.tre
> R --vanilla < convert_mccTree.r
> python asrCC.py
> python asrSounds.csv
> python evaluation.py