Site frequency spectrum (SFS)
Tajima's D analysis
If you find this tool useful, you can cite:
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Karagol, A., & Karagol, T. (2024). An Evolutionary Statistics Toolkit for Simplified Sequence Analysis on Web with Client-Side Processing. bioRxiv, 2024-08. doi: https://doi.org/10.1101/2024.08.01.606148
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Tajima, F. (1989). Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123:585-595.
Shannon's Entrophy (H)
Calculation
If you find this tool useful, you can cite:
-
Karagol, A., & Karagol, T. (2024). An Evolutionary Statistics Toolkit for Simplified Sequence Analysis on Web with Client-Side Processing. bioRxiv, 2024-08. doi: https://doi.org/10.1101/2024.08.01.606148
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Shannon, C.E. (1948) A Mathematical Theory of Communication. Bell System Technical Journal, 27, 379-423.
http://dx.doi.org/10.1002/j.1538-7305.1948.tb01338.x
Alignment processor for pairwise variation analysis
If you find this tool useful, you can cite:
Karagol, A., & Karagol, T. (2024). An Evolutionary Statistics Toolkit for Simplified Sequence Analysis on Web with Client-Side Processing. bioRxiv, 2024-08. doi: https://doi.org/10.1101/2024.08.01.606148
Wave function
If you find this tool useful, you can cite:
Karagol, A., & Karagol, T. (2024). An Evolutionary Statistics Toolkit for Simplified Sequence Analysis on Web with Client-Side Processing. bioRxiv, 2024-08. doi: https://doi.org/10.1101/2024.08.01.606148
Pair frequencies
This tool utilizes array format for the calculation.
Example format:
To convert your Clustal Alignment to array format:
If you find this tool useful, you can cite:
Karagol, A., & Karagol, T. (2024). An Evolutionary Statistics Toolkit for Simplified Sequence Analysis on Web with Client-Side Processing. bioRxiv, 2024-08. doi: https://doi.org/10.1101/2024.08.01.606148
Thank you for visiting this site. The toolkit is freely available for academic and non-commercial use.
Please contact for commercial usage.
visits since Jul 29 2024.
All rights reserved @Alper Karagöl, @Taner Karagöl
*Google Colab notebooks and open source codes are available at:
Site frequency spectrum (SFS) & Tajima's D analysis:
https://github.com/karagol-alper/SFS-Tajima-s-D
Shannon's Entrophy (H) Calculation:
https://github.com/karagol-alper/Shannon-s-Entrophy-H
Alignment processor for pairwise variation analysis:
https://github.com/karagol-alper/Aln-to-matrix
https://github.com/karagol-taner/HGVS-missense-variants-to-FASTA
Wave function:
https://github.com/karagol-alper/Pair-frequencies
Pair frequencies: