Bioinformatics/Sequence Treatment
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This Part needs to be reorganized in order to better balance the information between chapters; the present chapter order hews to a no-longer extant narrative structure.
Chapter One consists of a thorough introduction to Bayes Theorem and the concepts of Maximum Likelihood and Maximum Parsimony.
Chapter Two through Four will include (after being redivided) discussion of the constraints under which sequences evolve, with many references to the structural discussions from Part I. There will be a description of what a multiple sequence alignment is; it will include a full description of the algorithms used by Clustal and BLAST.
Chapter Five will introduce distinct cases of alignment were structural information is known. This extends from cases were
I have an entire chapter devoted to Gene Transfer since I've been working on that question lately.
The final chapter will be devoted to the question of what you can meaningfully predict using different amounts of information.
