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Software
 
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.
 
QSCORE >
Compare two multiple alignments for benchmarking.
  PALS >
Whole-genome alignment.
 
PREFAB >
Protein Reference Alignment Database.
  MSA benchmark collection >
Selected multiple alignment benchmarks in a standardized FASTA format.