Computes Tajimas D, the Pi- or Watterson-Estimator for multiple sequences.

## Project description

Compute the Tajima's-D, Pi-Estimator or Watterson-Estimator for multiple sequences.

Tajima's D is a population genetic test statistic that computes the difference between the mean number of pairwise differences and the number of segregating sites. It is used to determine whether a population is expanding or shrinking.

## Tajima's D

Tajima's D is defined as follows:

If , there are many rare variants, indicating an expanding population.

Whereas , indicates an declining population as there are many intermediate variants.

A result is consideres significant if or .

## Pi-Estimator

The π estimator is the average number of pairwise differences between any two sequences:

## Watterson-Estimator

The Watterson estimator is the expected number of segregating sites.

## Installation

Using pip / pip3:

pip install tajimas_d


Using conda:

conda install -c bioconda tajimas_d


Or by source:

git clone git@github.com:not-a-feature/tajimas_d.git
cd tajimas_d
pip install .


## How to use

from tajimas_d import tajimas_d, watterson_estimator, pi_estimator

sequences = ["AAAA", "AAAT", "AAGT", "AAGT"]

theta_tajima = tajimas_d(sequences)
theta_pi = pi_estimator(sequences)
theta_w = watterson_estimator(sequences)


## Standalone version

The standalone version requires miniFasta>=2.2 to be installed.

usage: tajimas_d [-h] -f PATH [-p] [-t] [-w]

tajimas_d: Compute Tajima's D, the Pi- or Watterson-Estimator for multiple
sequences.

optional arguments:
-h, --help            show this help message and exit
-f PATH, --file PATH  Path to fasta file with all sequences.
-p, --pi              Compute the Pi-Estimator score.
-t, --tajima          Compute the Pi-Estimator score. (default)
-w, --watterson       Compute the Watterson-Estimator score.



Copyright (C) 2024 by Jules Kreuer - @not_a_feature

This piece of software is published unter the GNU General Public License v3.0 TLDR:

Permissions Conditions Limitations
✓ Commercial use Disclose source ✕ Liability
✓ Patent use State changes
✓ Private use

Go to LICENSE.md to see the full version.

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