Table 1 Abbreviations used in the text
From: Secondary structure information does not improve OTU assignment for partial 16s rRNA sequences
Abbreviation | Definition |
|---|---|
DOTUR | A software package, mainly used for clustering sequences |
ESPRIT | A hierarchical clustering algorithm, mainly used for clustering sequences |
ESPRIT-Tree | The fast version of ESPRIT |
INFERNAL | A sequence alignment algorithm considering secondary structures |
MOTHUR | An improved version of DOTUR for analyzing sequences |
MSA | Multiple sequence alignment |
NMI | Normalized mutual information. A metric to evaluate clustering performances |
NW | Needleman–Wunsch algorithm, a widely used global sequence alignment algorithm |
OTU | Operational taxonomic units |
PARTS | A sequence alignment algorithm considering secondary structures |
PSA | Pairwise sequence alignment |
TaxCollector | A set of Python scripts that attaches taxonomic information to sequences in a database |
TD | Taxonomy-dependent (clustering method) |
TI | Taxonomy-independent (clustering method) |
