Site frequency spectrum (SFS)
Tajima's D analysis
If you find this tool useful, you can cite:
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Karagöl, T., Karagöl, A. Basic Bioinformatics Toolkits (manuscript in preparation)
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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:
-
Karagöl, T., Karagöl, A. Basic Bioinformatics Toolkits (manuscript in preparation)
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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:
-
Karagöl, T., Karagöl, A. Basic Bioinformatics Toolkits (manuscript in preparation)
Wave function
If you find this tool useful, you can cite:
-
Karagöl, T., Karagöl, A. Basic Bioinformatics Toolkits (manuscript in preparation)
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:
-
Karagöl, T., Karagöl, A. Basic Bioinformatics Toolkits (manuscript in preparation)
All rights reserved @AlperKaragol, @Taner karagöl
*Google Colab notebooks and open source codes are available at GitHub:
Site frequency spectrum (SFS) & Tajima's D analysis:
https://github.com/karagol-alper
Shannon's Entrophy (H) Calculation:
https://github.com/karagol-alper
Alignment processor for pairwise variation analysis:
https://github.com/karagol-alper
https://github.com/karagol-taner/HGVS-missense-variants-to-FASTA
Wave function:
https://github.com/karagol-alper
Pair frequencies: