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

This module is now part of the bfx suite. See https://py-bfx.readthedocs.io for more information.

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: $\theta_\text{Tajima}=\frac{\theta_{\pi}%20-%20\theta_{W}}{\sqrt{\text{Var}(\theta_{\pi}-\theta_{W})}}$

If $\theta_\text{Tajima}<0$, there are many rare variants, indicating an expanding population.

Whereas $0<\theta_\text{Tajima}$, indicates an declining population as there are many intermediate variants.

A result is consideres significant if $\theta_\text{Tajima}<-2$ or $2<\theta_\text{Tajima}$.

Pi-Estimator

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

$\theta_{\pi}=\frac{\text{Nr. of pairwise differences}}{\binom{n}{2}}$

Watterson-Estimator

The Watterson estimator is the expected number of segregating sites.

$\theta_{W}=\frac{\text{Nr. of segregating sites}}{\Sigma_{i=1}^{n-1}\frac{1}{i}}$

Installation

Using pip / pip3:

pip install tajimas_d

Using conda:

conda install -c bioconda tajimas_d

Or by source:

git clone [email protected]: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.

License

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
✓ Distribution	License and copyright notice	✕ Warranty
✓ Modification	Same license
✓ Patent use	State changes
✓ Private use

Go to LICENSE.md to see the full version.