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..
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| 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.
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Anchor Trimming:
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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.
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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).
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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.
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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
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