A hybrid summary method for reconstructing species tree from gene trees.
Project description
FASTRAL
Description
FASTRAL is a novel approach for running 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) 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.
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FASTRAL-0.5.7.tar.gz
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