Comparison of speed and accuracy of MLgsc versus classifying methods implemented in Mothur for the 16S rRNA gene.

(a) For the Mothur methods, a query was considered not classifiable if the corresponding output line did not indicate a genus (g__ prefix). For MLgsc, a query was considered not classifiable if any node in the corresponding output line had an evidence ratio (ER) below the cutoff. The use of evidence ratio do detect sequences that are not confidently classified is described in section Procedure, subsection Validation.
(b) Mothur command: classify.seqs(fasta = aln, template = gg_13_8_99.fasta, taxonomy = gg_13_8_99.gg.tax, iters = 1000, method = wang, ksize = 8, processors = 1)
(c) Mothur command: classify.seqs(fasta = aln1, template = gg_13_8_99.fasta, taxonomy = gg_13_8_99.gg.tax, iters = 1000, method = knn, numwanted = 10, search = kmer, ksize = 8, processors = 1)
(d) Mothur command: classify.seqs(fasta = aln2, template = gg_13_8_99.fasta, taxonomy = gg_13_8_99.gg.tax, iters = 1000, method = knn, numwanted = 10, search = blast, processors = 1)
(e) Mothur command: classify.seqs(fasta = aln3, template = gg_13_8_99.fasta, taxonomy = gg_13_8_99.gg.tax, iters = 1000, method = knn, numwanted = 10, search = suffix, processors = 16)
(f) MLgsc command: mlgsc-A 16S.fasta 16S_classifier.bcls
Comparison of speed and accuracy of MLgsc versus classifying methods implemented in Mothur for the 16S rRNA gene.