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).

pairs_local command

Aligns pairs of sequences in a FASTA file using local alignment. The first two sequences (1st and 2nd) are aligned, then the second pair (3rd and 4th) and so on up to the N-1th and Nth sequence. To align all-vs.-all, use allpairs_local. Alignments are constructed and reported unconditionally; accept and termination conditions are not supported. More than one alignment may be reported for a given pair. Multithreading is not supported, but this feature could be added.

Example

usearch -pairs_local pairs.fasta -alnout results.aln