astral_runner.py

Generate input files and infer a coalescent-based species tree with ASTRAL-III.

astral_runner.py.py [OPTIONS] -i <input_directories>

Required arguments:

  • -i, --input <input_directory> Path to directory containing single gene trees and their corresponding bootstrap value files.

Optional arguments:

  • -o, --output <out_dir> Path to user-defined output directory.
    • Default: ./astral_runner_<M.D.Y>
  • -p, --prefix <prefix> Prefix of input files.
    • Default: NONE
    • Example: path/to/input/prefix*
  • -s, --suffix <suffix> Suffix of input files.
    • Default: NONE
    • Example: path/to/input/*suffix
  • -h, --help Show this help message and exit.

Default astral_runner.py output:

  • a file all_sgt.tre that contains:
    • all single gene trees provided in Newick format.
  • a file bs_files.txt that contains:
    • paths to all ML bootstrap files.
  • a file astral_BS.out that contains:
    • 100 bootstrapped replicate trees.
    • A greedy consensus of the 100 bootstrapped replicate trees.
    • The “main” ASTRAL tree.

NOTE: Users may choose to use the trees generated by sgt_constructor.py using the ortholog files generated by matrix_constructor.py. For example, sgt_constructor.py –trees_only -i matrix_constructor_out_<M.D.Y>/trimal/ -o <above, directory of your choice>/. If users construct trees via this method, example run is astral_runner.py -i sgt_constructor_out_<M.D.Y>/trees/.