WARACS

WARACS: Wrappers to Automate the Reconstruction of Ancestral Character States

- Compatibility

• Python v.2.7 (https://www.python.org/download/releases/2.7/)
• Python v.3.5 (https://www.python.org/downloads/release/python-350/)

- Prerequisites

• Python package DendroPy (https://pypi.python.org/pypi/DendroPy)
• Python package numpy (https://pypi.python.org/pypi/numpy)
• Python package six (https://pypi.python.org/pypi/six)

- Wrapped Applications

• Mesquite (http://mesquiteproject.org)
• BayesTraits (http://www.evolution.reading.ac.uk/BayesTraits.html)
• TreeGraph2 (http://treegraph.bioinfweb.info/)

- Usage under Linux and Mac OS

1. Test the wrapper

python /path_to_WARACS/WARACS_Mesquite.py -h

2. Perform an ancestral character state reconstruction via Mesquite

python /path_to_WARACS/WARACS_Mesquite.py
  -c /path_to_input/character_state_distribution.csv
  -t /path_to_input/tree_distribution.tre
  -p /path_to_input/plotting_tree.tre
  -o likelihood
  -n 2
  -s /path_to_Mesquite/mesquite.sh
  -v True

3. Perform an ancestral character state reconstruction via BayesTraits

python /path_to_WARACS/WARACS_BayesTraits.py
  -c /path_to_input/character_state_distribution.csv
  -t /path_to_input/tree_distribution.tre
  -p /path_to_input/plotting_tree.tre
  -n 1
  -o likelihood
  -s /path_to_BayesTraits/BayesTraitsV2
  -v True

4. Visualize the character state reconstruction results via TreeGraph2

python /path_to_WARACS/WARACS_TreeGraph2.py
  -r /path_to_input/tree_distribution__Mesquite_likelihood_char2.csv
  -p /path_to_input/tree_distribution__Mesquite_likelihood_char2.tre
  -d /path_to_input/color_dictionary.csv
  -c /path_to_input/character_state_distribution.csv
  -n 2
  -s /path_to_TreeGraph2/TreeGraph.jar
  -v True

- Usage under Windows

Testing the wrapper; the other commands work correspondingly

C:\Python\python.exe \path_to_WARACS\WARACS_Mesquite.py -h