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Added the cluster workflow to cluster protein sequences.
Added the realign workflow to generate clustering output.
Added the recluster workflow to correct errors in clusterings.
Added the reassign workflow to reassign cluster members to their closest centroid.
Added the option -M/--memory-limit to set a memory limit for clustering workflows.
Added the --approx-id option to filter alignments by approximate sequence identity and to set an approximate sequence identity threshold for clustering.
Added the --member-cover option to set the coverage threshold of the cluster member sequence.
Added the --cluster-steps option to set steps for cascaded clustering.
Added the --clusters option to specify clustering input file.
The blastx mode will now mask any open reading frame below the minimum required length as specified by --min-orf.
The blastx mode will only count unmasked letters towards the block size.
Fixed a bug that caused an error when using the global ranking mode.
Added the fast mode as the first round in iterative searches.
Fixed a bug that caused the program not to function on systems without support for SSE4.1.
Improved multi-threaded load balancing of gapped extension computations.
Improved performance of seed extension stage when HSP filter settings are used.
Added the option --soft-masking with possible values 0 and tantan to permit soft-masking using the tantan algorithm.
Fixed a bug that could cause an inflate error in multiprocessing mode.
Added the option --swipe to compute full Smith Waterman alignments of all queries against all targets.
Added the sensitivity mode --faster.
Added the output fields approx_pident and corrected_bitscore to the tabular format.
Added the --lin-stage1 option to linearize comparisons in the seeding stage by only considering hits against the longest query sequence for identical seeds (only supported when compiled with -DEXTRA=ON).
Added the --kmer-ranking option to rank sequences when --lin-stage1 is used (only supported when compiled with -DKEEP_TARGET_ID=ON).
Added the option --no-block-size-limit to deactivate upper limits for the block size when the --memory-limit option is used.
Added the greedy-vertex-cover workflow to compute clustering based on alignments.
Added the --edge-format option to set edge format for greedy vertex cover.
Added the --edges option to set input file for greedy vertex cover.
Added the --centroid-out option to output centroid sequences for greedy vertex cover.
Added the --unaligned-targets option to generate an output file of unaligned targets.
Fixed an issue that failed compilation using the Intel Compiler.
Fixed an issue that could cause a segmentation fault in rare cases.
The --header option can now be used with the parameter simple to enable simple headers for the tabular format, or without a parameter to enable headers for the clustering format.
Added the option --mp-self to optimize self-alignment in multiprocessing mode.
Added the option --query-or-subject-cover to report alignments if the query or the subject cover (or both) are above the given threshold.
Removed support for the --comp-based-stats 2 option (now equivalent to --comp-based-stats 3).
Removed hit culling in case of overlapping target ranges in frameshift alignment mode.
Added the option --anchored-swipe to activate anchored SWIPE extension.