| | Mothur | QIIME | CBD |
|---|
Interface | Command line | Command line | Web or command line |
OTUs | Yes | Yes | No |
Alignment | Yes | Yes | No |
Phylogenetic tree | Yes | Yes | No |
Software | Yes | Yes | No |
Parameters | Yes | Yes | No |
- “Interface” indicates how a user communicates with a computer; “OTUs” indicates that clustering methods or algorithms, such as cd-hit, BLAST, furthest neighbor and nearest neighbor, must assign similar sequences to operational taxonomic units (OTUs) to generate a distance matrix; “Alignment” indicates methods such as PyNAST, MUSCLE, and SILVA required to align sequences for generating a distance matrix; “Phylogenetic tree” indicates methods such as FastTree are needed to produce a phylogenetic tree to generate a distance matrix; “Software” indicates a user needs to select different methods or algorithms for choosing OTUs, align sequences and build a phylogenetic tree; “Parameters” indicates a user must choose different parameters associated with a corresponding software.
