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Video talks on 16S data analysis posted.

URMAP ultra-fast read mapper posted (paper).

~20% of taxonomy annotations in SILVA and Greengenes are wrong (paper).

Taxonomy prediction is <50% accurate for 16S V4 sequences (paper).

97% OTU threshold is wrong for species, should be 99% for full-length 16S, 100% V4 (paper).
 

 
USEARCH >
Extreme high-throughput sequence analysis. Orders of magnitude faster than BLAST. 		  MUSCLE >
Multiple sequence alignment. Faster and more accurate than CLUSTALW.
 
UPARSE >
OTU clustering for 16S and other marker genes. Highly accurate OTU sequences and improved diversity measures.
   UCHIME >
Chimeric sequence detection.
 
PILER >
De novo genome repeat finder.
   PILER-CR >
Detection of CRISPR repeats in bacterial genomes.
 
URMAP  >> new
Ultra-fast read mapper. 		  PALS >
Whole-genome alignment.
 
PREFAB >
Protein Reference Alignment Database. 		  MSA benchmark collection >
Selected multiple alignment benchmarks in a standardized FASTA format.