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Fig. S1 Schematic diagram of the internal transcribed spacer (ITS) rDNA region and simulated fragments.

Fig. S2 Comparison of the time required to run BLAST searches and Statistical Assignment Program (SAP) analyses.

Table S1 Summary of next-generation sequencing platforms, number of reads produced, and read length

Table S2 List of species and corresponding GenBank accessions included in the test data set

Table S3 Query recovery comparison using BLAST, MEGAN, and Statistical Assignment Program (SAP) ConstrainedNJ (no cutoff enforced)

Table S4 Problematic sequences that were not correctly classified by BLAST, MEGAN, or the Statistical Assignment Program (SAP) ConstrainedNJ (no cutoff enforced)

Methods S1 Comparison of the time required to classify amplicons using the BH method and the Statistical Assignment Program (SAP).

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