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Table 1 Major functions of seven pipelines

From: A review of software for analyzing molecular sequences

Capabilities   Mothur Qiime Waters RD-Pipline VAMPS Genboree SnoWMAn
Documentation Available guides
Installation Shortcut option (instant download)      
  Native version: Mac OSX     
  Native version: Windows     
  Native version: Linux     
  Web based    
Updating Re-download entire program     
  Re-download updated sections        
Interface Command line      
  Graphical User Interface        
  Web form GUI    
Sequencing platforms Illumina
  454 Pyroseq
Preparing sequences Accepted file formats        
  sff * *    
  Fasta
  Quality score     
  Flow file data      
  User defined barcodes or primers
  User defined metadata
  Alignment
  Summary function      
  Trims barcodes and primers off of sequences
  Removes short reads
  Identify and remove chimeras
  Remove contaminants      
Approaches to analyze files OTU binning/clustering
  Phylotype binning     
  Phylogenetic tree     
Analysis output Alpha diversity
  Beta diversity
  Ecological indexes
  Unifrac
  Visualization
  1. *Not required but strongly suggested; Engineered for specific capability; Integrates other pipelines