DIAMOND v2.1.9

• Corrected the prefix of the query length field for the SAM format.
• Added the size modifiers 'T', 'M' and 'K' for the --memory-limit/-M option.
• Added the option --mutual-cover to cluster sequences by mutual coverage percentage of the cluster representative and member sequence.
• Added the option --symmetric for computing greedy vertex cover with symmetric edges.
• Fixed an issue that caused the --approx-id option and the approx_pident output field not to work correctly when using the --anchored-swipe option.
• Added the option --no-reassign to prevent reassignment to closest representative for the greedy vertex cover and clustering workflows.
• Added the option --connected-component-depth to activate clustering of connected components at a given maximum depth for the greedy vertex cover and the clustering workflows.
• Fixed a compiler error for Clang v17.
• Improved search performance when searching with mutual coverage threshold by filtering for sequence length ratio.
• Added the sensitivity mode --shapes-30x10 with sensitivity approximately equivalent to --mid-sensitive.
• Added the options --round-coverage and --round-approx-id to set per round cutoffs for cascaded clustering.
• The CMake switch -DKEEP_TARGET_ID is now obsolete and the corresponding function is always available.
• Added the option --include-lineage to the taxonomic classification format to include taxonomic lineage in the output.
• Added native support for the ARM NEON instruction set (contributed by @althonos).

DIAMOND v2.1.8

• Fixed an issue that could cause reduced performance when running in query-indexed mode.
• Added support for the JSON output format (option -f json-flat).
• Added the option --sam-query-len to output query length in SAM format.

DIAMOND v2.1.7

• Fixed a bug that caused taxonomy names not to be loaded correctly for the makedb workflow.
• Fixed a bug that caused a crash when using the --target-indexed option.
• Fixed an error when using the --tmpdir option for the makedb workflow.
• Added a warning message when sequence accessions are shortened due to parsing rules for the makedb workflow.
• Added the option --no-parse-seqids to disable parsing of sequence accessions.
• Changed the command line help to print options separated by command.
• Fixed an issue that the --ignore-warnings option could not be used for the makedb workflow.

DIAMOND v2.1.6

• Fixed compatibility issues on older systems without support for AVX2.
• Fixed linker errors when compiled with -DX86=OFF.
• Fixed a compiler error on macOS systems.
• Fixed a bug that could cause missing tags in the XML output format and unaligned queries not to be reported correctly.
• Fixed a bug that caused the PAF output format not to work correctly.

DIAMOND v2.1.5

• Disabled the use of frequency based seed masking when using the linear-time search feature with respect to the targets.
• Fixed a bug that caused a Database file is not a BLAST database error message for the prepdb workflow.
• Fixed a bug that caused a segmentation fault when using BLAST databases.
• Added line numbers for error messages when reading taxonomy mapping files.
• Fixed a bug that could cause a crash when using the greedy-vertex-cover workflow without the --out and --centroid-out options.
• Fixed a bug that caused the greedy-vertex-cover workflow to only produce a trivial clustering.
• Fixed a bug that caused the last codon of the -2 reading frame to be translated incorrectly.
• Reduced the memory use of the clustering workflow.
• Updated the bundled NCBI toolkit to the latest version.

DIAMOND v2.1.4

• Leading spaces are now trimmed and tabulator characters escaped as \t in sequence titles, and a warning message is produced.
• Blank sequence titles are now replaced by N/A, and a warning message is produced.
• Fixed a bug that could cause a Traceback error in certain cases.
• Fixed a bug that caused the qlen and score output fields not to be reported correctly for the realign workflow.
• Added an error message when using unsupported output fields for the realign workflow.
• Fixed an issue that could cause a Missing fields in input line error when clustering.
• Optimized the performance of the linclust workflow.
• Reduced the memory use of the clustering workflow.
• Fixed a bug that caused using standard input as the query not to work.

DIAMOND v2.1.3

• Fixed compiler errors for GCC 4.8.
• Fixed a GCC compiler error.
• Fixed a segfault issue occuring when compiled using GCC 12 on ARM64 systems.
• Fixed an issue that caused missing support for AVX2.

DIAMOND v2.1.2

• The iterated search mode (option --iterate) now uses a linear-time feature as the first search round.
• Added the linclust command to cluster using only a single linear-time search round.
• Fixed compiler errors on macOS.
• Fixed a bug that caused invalid alignment traceback output for the DAA view workflow.
• Added the merge-daa workflow to merge DAA files.
• Fixed an error when using the --max-target-seqs/-k option for the DAA view workflow.
• Removed AVX2 support from the Windows release binary to ensure compatibility with older systems.
• Permitted the --ignore-warnings option for the cluster and deepclust workflows.
• Use unlinked temporary files for database blocks in clustering workflows.
• Fixed a bug that could cause invalid results when using a clustering step with linearization as the final round in combination with database processing in multiple super blocks.
• The --lin-stage1 option can now be used without compilation using the -DEXTRA=ON cmake option.
• Added the option to specify the _lin suffix for sensitivity keywords for the --iterate option to activate linear-time feature.
• Added the option --linsearch to activate linear-time feature for the search workflows.
• Fixed a bug that caused the ppos and positive output fields not to work for the realign workflow.
• Fixed an issue that caused motif masking not to work when compiled with link time optimization.

DIAMOND v2.1.1

• Fixed compilation errors on non-x86 systems and for the clang compiler.
• Fixed an error message when running the recluster workflow.
• Fixed a bug that could cause an invalid varint encoding error when using the DAA format.
• Fixed a bug that could cause corrupted DAA output.
• Fixed a bug that caused an error in the view workflow.
• Adjusted the hit culling heuristic of the frameshift alignment mode to be less aggressive.

DIAMOND v2.1.0

• 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.