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README.md

WARACS

WARACS: Wrappers to Automate the Reconstruction of Ancestral Character States

- Compatibility

- Prerequisites

- Wrapped Applications

- 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

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WARACS: Wrappers to Automate the Reconstruction of Ancestral Character States

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