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).

allpairs_local command

Makes pair-wise all-vs.-all alignments of all pairs in a FASTA file. Alignments are local. No index is used. More than one alignment may be reported for a given pair.

You must either specify the -acceptall option, which aligns all pairs (except those for which no HSP is found), or accept options.

Example

usearch -allpairs_local seqs.fasta -alnout results.aln