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 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 .
The π estimator is the average number of pairwise differences between any two sequences:
The Watterson estimator is the expected number of segregating sites.
Using pip / pip3:
pip install tajimas_d
conda install -c bioconda tajimas_d
Or by source:
git clone email@example.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)
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) 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.
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.
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