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Software

MBL Software
GAST:


  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.

  Citation:

        
   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.
.

SLP:


  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.

  Citation:

        
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 https://github.com/meren/454-anchor-trimming.

   A static snapshot of the codebase and description are also available here.




Other Useful Software

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

ESPRIT:
  An algorithm for estimating species richness using large collections of 16S rRNA pyrosequences.

fasta2pfam.pl: 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).

MOTHUR:
  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.

MUSCLE:
  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.

Usearch:
  Suite of high-throughput sequence analysis algorithms.

Uchime:
  Identifying chimeras.
Otupipe:
  OTU clustering pipeline for next-gen reads