tajimas-d 1.0.4

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

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

Or by source:

git clone [e-mail]: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

Clone the repository and cd into it. Intall the requirements (miniFasta >= 2.2, for fasta reading).

usage: tajimas-d.py [-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) 2022 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.

Dependencies

In addition to packages included in Python 3, this piece of software uses 3rd-party software packages for development purposes that are not required in the published version. Go to DEPENDENCIES.md to see all dependencies and licenses.