VSEARCH version 1.1.1

Added info about --log and --quiet options to the help text.

VSEARCH version 1.1.0

VSEARCH 1.1.0: Support for options --quiet and --log

VSEARCH version 1.0.16

Integrate patches to the code from Debian

VSEARCH version 1.0.15

Fix bug in calculation of identity metric between sequences when using the MBL definition (--iddef 3).

VSEARCH version 1.0.14

VSEARCH 1.0.14: Fix for ignored strand in multiple sequence alignment after clustering

VSEARCH version 1.0.13

VSEARCH 1.0.13 fixes a memory allocation problem with multiple sequence alignments with clustered sequences and a memory leak. It also increases the maximum FASTA header line length to 4MB.

VSEARCH version 1.0.12

VSEARCH version 1.0.12 has a temporary fix for long FASTA header lines.

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.