SAI

sai is a Python package for Statistics for Adaptive Introgression. It detects candidate regions of adaptive introgression from population genomic datasets. Currently, it supports the calculation of the number of uniquely shared sites (U statistic) and the quantile statistic (Q statistic) proposed by Racimo et al. (2017). sai does not require phased data, and supports an arbitrary number of source/donor populations (i.e., populations assumed to provide introgressed material) and arbitrary ploidy.

Requirements

sai works on Linux operating systems and tested with the following:

- matplotlib=3.9.1
- natsort=8.4.0
- numpy=1.26.4
- pandas=2.2.1
- pysam=0.23.0
- python=3.9.19
- pytest=8.1.1
- scikit-allel=1.3.7
- scipy=1.12.0

Installation

Users can first install mamba, and then install sai using the following commands:

git clone https://github.com/xin-huang/sai
cd sai
mamba env create -f build-env.yaml
mamba activate sai
pip install .

Help

To get help information, users can use:

sai -h

This will display information for three commands:

Command	Description
score	Run the score command based on specified parameters
outlier	Detect and output outlier rows based on quantile thresholds
plot	Generate a scatter plot of U vs Q statistics

If you need further help, such as such as reporting a bug or suggesting a feature, please open an issue.