VSEARCH version 1.0.11

VSEARCH 1.0.11 can write results to files in SAM format.

VSEARCH version 1.0.10

VSEARCH 1.0.10 incorporates a number of fixes and changes:

• fix for bug in alignment in rare cases
• fix for alignment of long sequences (>15000bp)
• fix for lack of detection of under- or overflow in SIMD aligner
• default maxseqlength set to 50000
• new linear memory aligner for alignment of longer sequences reduces memory requirements
• a new cluster_size command that sorts sequences by decreasing abundance before clustering
• cluster_fast will now sort sequences by decreasing length, then by decreasing abundance and finally by sequence identifier
• help messages for clustering have been improved
• in uc files, perfect alignment is indicated with "=" sign
• meaning of userfields qlo, qhi, tlo, thi changed for compatibility with usearch; new userfields qilo, qihi, tilo, tihi gives coordinates ignoring terminal gaps
• a few other small fixes

Alignment of long sequences is slow because it is performed by an exact and optimal algorithm. VSEARCH works best with sequences less than 5000 bp long, but should now work correctly with longer sequences as well.

These changes were originally introduced in version 1.0.8, but there were no official releases for 1.0.8 and 1.0.9.

VSEARCH version 1.0.7

Fixed bug in output from chimera detection with --uchimeout option, reduced default for --maxseqlength option, and removed some compiler warnings.

VSEARCH version 1.0.6

Fixed a memory allocation bug in chimera detection.

VSEARCH version 1.0.5

Fix minor bug with --allpairs_global and --acceptall.

VSEARCH version 1.0.4

Added --allpairs_global option for all-vs-all pairwise optimal global alignment. Reduced memory requirements slightly. Removed memory leaks.

VSEARCH version 1.0.3

Minor change: Option --help now writes output to stdout.

VSEARCH version 1.0.2

Bug fixes (ssse3/sse41 requirement, memory leak). AMD cpus should work well now.

VSEARCH version 1.0.1

Bug fixes (sortbysize, semicolon after size annotation in headers) and minor changes (labels as secondary sort key for most sorts, treat T and U as identical for dereplication, only output size in dbmatched file if sizeout specified).

VSEARCH version 1.0.0

First public release of VSEARCH