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>
- Default:
-p
,--prefix <prefix>
Prefix of input files.- Default:
NONE
- Example:
path/to/input/prefix*
- Default:
-s
,--suffix <suffix>
Suffix of input files.- Default:
NONE
- Example:
path/to/input/*suffix
- Default:
-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/
.