List of Figures

1. GC base composition in P. sojae and infected G. max libraries
2. Dissimilarity distributions for P. sojae and infected G. max libraries
3. Pairwise dissimilarity for P. sojae and infected G. max libraries
4. Cumulative dissimilarity distributions for M. truncatula libraries
5. Pairwise dissimilarity for M. truncatula libraries
6. Accumulation curves for MHAM mycorrhizal root transcripts
7. Frequency distributions used to test diversity estimators
8. Example identity matrix
9. Diversity estimates as a function of sample size
10. Estimator accuracy validation
11. Estimated diversity in M. truncatula libraries
12. Effect of increasing sample size on empirical diversity estimates
13. Dendrogram of libraries, grouped by complementarity
14. Paired dissimilarity test results from validation sequences
15. Calibration and confidence functions
16. Calibration, confidence, and comparison curves
17. Paired dissimilarity test results from transcript libraries
18. Length-scaled paired dissimilarity test results
19. GC content of training sets, validation sequences, and test libraries
20. Dendrogram of one plant and three fungal libraries
21. Dendrogram of fungal and plant pure- and mixed-culture libraries
22. Identity matrix using BLASTN and $E<10^{-10}$
23. Dendrogram using BLASTN and $E<10^{-10}$
24. Identity matrix using BLASTN and $E<10^{-2}$
25. Dendrogram using BLASTN and $E<10^{-2}$
26. Identity matrix using TBLASTX and $E<10^{-2}$
27. Dendrogram using TBLASTX and $E<10^{-2}$