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1.11 Mathematical Specifics and Computational Implementations
Throughout the text an effort is made to provide mathematical specifics to clearly understand the theoretical underpinnings of the methods. This provides a strong exposition of the theory but the motivation for this is not to do more theory, but to then proceed to a clearly defined computational implementation. This is where mathematical elegance meets implementation/computational practicality (and the latter wins). In this text, the focus is almost entirely on elegent methods that also have highly efficient computational implementations.
2 Probabilistic Reasoning and Bioinformatics
In this chapter, a review is given of statistics and probability concepts, with implementation of many of the concepts in Python. Python scripts are then used to do a preliminary examination of the randomness of genomic (virus) sequence data. A short review of Linux OS setup (with Python automatically installed) and Python syntax is given in ssss1.