Metadata-Version: 2.1
Name: FASTRAL
Version: 0.5.9
Summary: A hybrid summary method for reconstructing species tree from gene trees.
Home-page: https://github.com/PayamDiba/FASTRAL
Author: Payam Dibaeinia
Author-email: dibaein2@illinois.edu
License: MIT License
Description: # FASTRAL
        
        ## Description
        FASTRAL is a novel approach for running [ASTRAL](https://github.com/smirarab/ASTRAL), a widely used and popular species tree reconstruction method. FASTRAL runs up to ~800 times faster than ASTRAL but with a similar (or sometimes better) accuracy.
        
        ## Getting Started
        To download FASTRAL, use the following command:
        
        ```pip install FASTRAL```
        
        Alternatively, you can clone this repo and run fastral_infer.py (see the bottom of this page).
        
        ## Usage
        To get a quick help on the required flags for running ASTRAL, run:
        
        ```fastral -h```
        
        The required flags for running FASTRAL are described below:
        
        * --ns: Number of sub-samples to be created. To specify multiple samples (containing different number of gene trees) use comma separated values
        * --nt: Number of trees per sample, if there are multiple samples use comma separated values
        * --k: Total number of input gene trees.
        * --it: Path to input gene trees
        * --os: Path for writing sampled trees
        * --aggregate: Path for writing aggregated species trees
        * --o: Path for writing FASTRAL output species tree
        * --time: Path for writing running times
        
        The following flags are optional:
        * --rep: If specified, samples are created with replacement | Default (if not specified): Samples are created without replacement
        * --path_ASTRID: path to ASTRID's runtime | Default: linux runtime of ASTRID-2 ([version untagged-fdc5326080d364b87c5a](https://github.com/pranjalv123/ASTRID/releases/tag/untagged-fdc5326080d364b87c5a)) is used
        * --path_ASTRAL: Path to ASTRAL's runtime | Default: modified ASTRAL 5.7.3 is used
        * --heuristics: Heuristics level of ASTRAL (See ASTRAL's manual) | Default: 0
        * --multi: Required if input gene trees contain multiple individuals. Specify the path to the mapping file
        * --incomp_id: (In multi-individual mode; optional) Path to a file containing the IDs of incomplete gene trees (zero-based). If specified, sampling step makes sure that each sub-sample contains at least one complete gene trees.
        
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Description-Content-Type: text/markdown
