– Runs ancestral state reconstruction given a tree and trait table


Provides a common interface for running various ancenstral state reconstruction methods (e.g. ACE, BayesTraits, etc.).

Usage: [options]

Input Arguments:



-t, --input_tree_fp
The tree to use for ASR
-i, --input_trait_table_fp
The trait table to use for ASR


-m, --asr_method
Method for ancestral state reconstruction. Valid choices are: ace_ml, ace_reml, ace_pic, wagner [default: ace_pic]
-o, --output_fp
Output trait table []
-c, --output_ci_fp
Output table containing 95% confidence intervals, loglik, and brownian motion parameters for each asr prediction []
-p, --parallel
Allow parallelization of asr
-j, --parallel_method
Method for parallelizaation. Valid choices are: sge, torque, multithreaded [default: sge]
-n, --num_jobs
Number of jobs to be submitted (if –parallel). [default: 100]
-d, --debug
To aid with debugging; get the command that the app controller is going to run


A table containing trait information for internal nodes of the tree.

Example 1:

Provide a tree file and trait table file: -i -t pruned_tree.newick -o -c