Global Alignment for Sequence Taxonomy
  - uses a reference database of SSU sequences to determine the taxonomy of hypervariable region tags.

  Available GAST-formatted SSU reference sets.


   Huse SM, Dethlefsen L, Huber JA, Mark Welch D, Relman DA, et al. (2008)
       Exploring Microbial Diversity and Taxonomy Using SSU rRNA Hypervariable Tag Sequencing.
       PLoS Genetics 4: e1000255.


  Single-Linkage Preclustering for improved OTU clustering
  - based on pairwise distances this is used as a preliminary
  step before average linkage clustering of short (<250nt) sequences.


Huse, SM, Mark Welch, D, Morrison, HG, and Sogin, ML (2010) Ironing out the wrinkles in the rare
       biosphere through improved OTU clustering. Environmental Microbiology (2010) 12(7), 1889-1898

Anchor Trimming:

  The latest version of Anchor Trimming software can be obtained from
Other Useful Software

  A graphical program for 16S rRNA alignments, and, with SILVA, the source of our reference
   set of aligned full-length rRNA sequences, RefSSU.

  An algorithm for estimating species richness using large collections of 16S rRNA pyrosequences. Converts a fasta file to pfam format for use with quickdist (uses bioperl libraries, and so can only be used if you have bioperl installed).

  A bioinformatics package which includes functions from DOTUR, SONS, TreeClimber,
   S-Libshuff and Unifrac. MOTHUR provides OTU clustering capabilities as well as diversity
   and rarefaction calculations used by VAMPS.

  Multiple Sequence Comparison by Log-expectation
    - a multiple sequence aligner optimized for extremely large datasets.

quickdist: Calculates a matrix of pairwise distances between sequences in a multiple sequence alignment.

RDP Classifier:
  Ribosomal Database Project Classifier:
    - associates hierarchical taxonomy (Bergey's manual) to 16S rRNA sequences.

  Suite of high-throughput sequence analysis algorithms.

  Identifying chimeras.
  OTU clustering pipeline for next-gen reads