Polyphest: Fast Polyploid Phylogeny Estimation

Installation

git clone https://github.com/NakhlehLab/Polyphest.git
cd Polyphest

python3 -m venv venv
source venv/bin/activate

pip install -r requirements.txt

Usage

python Polyphest.py --gene_tree_file PATH_TO_GENE_TREE --consensus_multiset_file PATH_TO_MULTISET --filter_strategy STRATEGY [OPTIONS]

Required Arguments

• --gene_tree_file: Path to the input gene tree file. The gene tree should be multi-labeled.
• --consensus_multiset_file: Path to the consensus multiset file. This file should list the leaf labels of the species MUL-tree, with each label on a new line. Leaf labels in the gene tree must correspond to elements within this consensus multiset
• --filter_strategy: The filtering strategy to be used. Options include constant, percentile, median, and stddev.

Optional Arguments

• --output_dir: The directory where the results will be saved. If not specified, the current working directory will be used by default.
• --use_near_isomorphic: Enables the use of near isomorphic comparison. Set to False by default.
• --isomorphic_threshold: Sets the threshold for isomorphic comparison. The default value is 0.2.
• --percentile: Specifies the percentile for percentile filtering. This is required if --filter_strategy is set to percentile.
• --constant_value: Specifies the constant value for constant filtering. This is required if --filter_strategy is set to constant.

Filtering Strategies

Polyphest supports four filtering strategies for removing clusters with low frequencies:

• Constant Filtering: Applies a fixed threshold to filter clusters.
• Percentile Filtering: Dynamically sets the threshold based on a specified percentile of the frequency distribution.
• Median Filtering: Uses the median of frequencies multiplied by a scale factor as the threshold.
• Standard Deviation (StdDev) Filtering: Sets the threshold based on the standard deviation from the mean or median of frequencies.

Examples

Run Polyphest using the percentile filtering strategy:

python Polyphest.py --gene_tree_file ./example/gene_multree.newick --consensus_multiset_file ./example/consensus_multiset.txt --filter_strategy percentile --percentile 75 --use_near_isomorphic True --isomorphic_threshold 0.2

Run Polyphest using the constant filtering strategy with a specific threshold value:

python Polyphest.py --gene_tree_file ./example/gene_multree.newick --consensus_multiset_file ./example/consensus_multiset.txt --filter_strategy constant --constant_value 0.2 --use_near_isomorphic True --isomorphic_threshold 0.2