Kunin et al. 2008 continued
1. Marker gene analyses is AMPHORA
2. Evolutionary distance methods - like neighbor joining. Most phylogenetic tree building methods require evolutionary distance matrix. We are dealing with this because 1) we are using reference alignment, 2) some methods can deal with that by using NA (fastree method deals).
3. Bayesian (similar to liklihood) [model-based methods, people like them], neighborhood joining, maximum parsimony (based on statistical model of evolution).
4. Supervised clustering - give criteria on how put things into groups (Katie published papers on this). Where does DOTUR fall?
5. Genome sequence method like the Sims et al. (analysis of books) that Steve K. sent around
1. Upside don't throw out all of the data (30%, not 99.9%). But if one functional category more abundant, is it because it has a larger copy number?
2. James mentioned there is a neutral theory of copy number.