Alignment and clustering of phylogenetic markers - implications for microbial diversity studies

BMC Bioinformatics

Table 2 OTU sets closest to the annotated species clustering for each multiple sequence alignment.

	Correction	MSA	Clustering	Distance	OTUs	Ace	Chao1	Shannon	VI
	F84	ClustalW	fn	0.05	56	79	116	3.39	0.044
Optimal	F84	NAST	fn	0.06	56	78	176	3.39	0.054
	JC	MUSCLE	fn	0.06	54	69	132	3.37	0.068
Drosophila (host) [36]	JC	ClustalW	fn	0.03	70	109	162	3.49	0.087
Marine sponge [37]	F84	ClustalW	fn	0.03	70	109	162	3.49	0.087
Soil [11]	JC	NAST	fn	0.03	99	150	169	3.66	0.157
Deep sea biosphere [13, 38]	JC	MUSCLE	fn	0.03	96	396	466	4.66	0.190
Termite hindgut [39]	JC	NAST	fn	0.01	185	360	351	4.11	0.320

The "VI" column indicates the VI distance of each clustering from the annotated species clustering. Best methods chosen by our validation methodology for each MSA ("Optimal") are contrasted with five recently published methodologies. The "Correction" column corresponds to the evolutionary distance correction. Note that for the optimal methods using ClustalW and NAST alignments, the F84 and K2P corrections produced identical OTU sets because the distance matrices were very similar, though not identical. All methods in this table used furthest neighbor (fn) clustering. The Ace, Chao1, and Shannon diversity estimators are also provided.

ISSN: 1471-2105