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A new, fast implementation of algorithms used for the adaptive analysis of amino acid alphabets as described in
Philip, G. K., & Freeland, S. J. (2011). Did evolution select a nonrandom “alphabet” of amino acids? Astrobiology, 11(3), 235-240.
Ilardo, M., Meringer, M., Freeland, S., Rasulev, B., & Cleaves II, H. J. (2015). Extraordinarily adaptive properties of the genetically encoded amino acids. Scientific reports, 5, 9414.
Ilardo, M., Bose, R., Meringer, M., Rasulev, B., Grefenstette, N., Stephenson, J., Freeland, S., Gillams, R. J. , Butch C. J., & Cleaves, H. J. (2019). Adaptive properties of the genetically encoded amino acid alphabet are inherited from its subsets. Scientific reports, 9(1), 1-9.
Example program calls:
./CliAdaptiveAnalysis -i data/Table1913Aa4Prop.txt -n 100000
./CliAdaptiveAnalysis -i data/Table1913Aa4Prop.txt -n 100000000 -v
Features
- adaptive analysis
- subset sampler
- coverage calculator