Computes Tajimas D, the Pi or WattersonEstimator for multiple sequences.
Project description
Compute the Tajima'sD, PiEstimator or WattersonEstimator 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 .
PiEstimator
The π estimator is the average number of pairwise differences between any two sequences:
WattersonEstimator
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:notafeature/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
usage: tajimas_d [h] f PATH [p] [t] [w]
tajimas_d: Compute Tajima's D, the Pi or WattersonEstimator 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 PiEstimator score.
t, tajima Compute the PiEstimator score. (default)
w, watterson Compute the WattersonEstimator 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 3rdparty 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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