BMC Bioinformatics

Table 2 Alignment test

From: Estimation of bacterial diversity using next generation sequencing of 16S rDNA: a comparison of different workflows

	50 × 60 mutated (interleaved)			50 × 60 mutated (stacked)
	3%	5%	10%	3%	5%	10%
Reference expected values	59	57	52	59	57	52
CROP	1959	1954	1955	1865	1850	1850
ESPRIT	193	59	56	205	59	56
MAFFT+JC	141	101	85	132	113	113
MAFFT+MAFFT	2289	1708	80	2289	1777	1270
MAFFT+Mothur	261	119	96	279	121	121
Mothur+JC	2947	2947	2948	2985	2985	2985
Mothur+MAFFT	899	685	477	2999	2999	2999
Mothur+Mothur	1087	923	736	1100	930	888
Mothur+PreC+ JC	1198	1198	1198	1333	1333	1333
Mothur+PreC+MAFFT	1328	1328	1328	1346	1346	1346
Mothur+PreC+Mothur	1080	938	938	1087	940	915
MUSCLE+JC	70	59	44	2999	2999	2999
MUSCLE+MAFFT	2287	1707	80	2288	1785	1269
MUSCLE+Mothur	264	64	57	571	466	466
Otupipe	139	91	59	144	95	61
RDP	59	58	53	59	57	52

OTUs observed with each of the workflows analysed at distances of 3, 5 and 10% for the datasets containing 50 different mutated replicas of the 60 test sequences stacked or interleaved.

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ISSN: 1471-2105

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