Sequence Clustering and Mapping

[gregcaporaso]

• expand reference-based clustering discussion
• update plots at the end to be based on several different random subsets of Greengenes to plot average and variance
• add greedier cluster function
• port clustering code to scikit-bio
• get useful layout of 16S graph visualizations
• add all alignments as edges with metadata indicating whether they resulted in a cluster
• add some discussion of real world run time for OTU picking (several people asked questions about doing this iteratively - like iterative msa - which is interesting, but runtime would be a limiting factor)
• add discussion of why approximations are required (i.e., why can't you compute distances between all pairs of sequences, build a tree, and define OTUs based on clades in the tree?) - this should go in the top of the notebook so it's clear why we don't compare all sequences against all other sequences.
• add max_accepts and max_rejects options
• add optional kmer-based cluster pre-selection