DIAMOND v2.0.6

• Changed the computation of expected values to use the method described in Park, Y., Sheetlin, S., Ma, N. et al. New finite-size correction for local alignment score distributions. BMC Res Notes 5, 286 (2012).
• Enabled the use of a custom scoring matrix without having to specify the statistical parameters (option --custom-matrix).
• Added support for compositional matrix adjust as described in Yi-Kuo Yu, Stephen F. Altschul, The construction of amino acid substitution matrices for the comparison of proteins with non-standard compositions, Bioinformatics, Volume 21, Issue 7, 1 April 2005, Pages 902–911. Three additional modes have been added that can be enabled by setting --comp-based-stats (2,3,4) (the feature is not enabled by default and does not support translated searches at the moment).
• Fixed a bug that could cause incorrect alignment coordinates, gaps counts and sequence identities being reported by diamond view.
• Targets are sorted by bit score instead of e-value in the alignment output when the --top parameter is used.
• Disabled support of custom scoring matrices for the DAA format.
• Fixed a bug that caused the use of a custom scoring matrix not to function correctly.
• Fixed an issue that caused the portable binary not to function on systems that did not support AVX.
• Added the option --no-unlink to prevent unlinking of temporary files.

DIAMOND v2.0.5

• Fixed an issue that could cause high memory use in frameshift alignment mode.

DIAMOND v2.0.4

• Fixed a bug that could cause the --max-target-seqs/-k, --ext-chunk-size and --file-buffer-size options not to function correctly on macOS.

DIAMOND v2.0.3

• Added a new sensitivity mode that is between the default mode and the sensitive mode in sensitivity (option --mid-sensitive).
• Added counters for total number of reference blocks, shapes and index chunks to the status messages.
• Fixed a bug (persisting since v2.0.2) that could cause secondary HSPs within one target not to be reported if the --max-hsps option was used with a non-default setting.
• Fixed a bug that could cause an invalid error message with regard to the database format in certain cases.
• The --no-self-hits option is no longer supported in blastx mode.
• Changed the semantics of the --no-self-hits option to check for equality of both sequence and sequence id, independent of the computed alignment.
• The selection of the top hit when using --top will respect the identity, coverage and no-self-hits filter settings (does not apply when frameshift alignment is enabled).
• The inclusion criterion for --top is applied to the bit score instead of the raw score and is no longer affected by integer rounding (does not apply when frameshift alignment is enabled).
• Improved the accuracy of the ranking heuristic.
• Added the options --ext-chunk-size and --no-ranking to control the ranking heuristic.

DIAMOND v2.0.2

• Fixed a bug (persisting since v2.0.0) that could cause incomplete results in blastx mode.
• Reduced the use of temporary disk space.
• Fixed an issue that could cause long runtimes when using the --taxon-list option.

DIAMOND v2.0.1

• Added feature for using the tool in a distributed computing environment. (See here for details: http://www.diamondsearch.org/index.php?pages/distributed_computing/)
• Fixed an issue that could cause increased memory usage and runtimes in certain cases.
• Fixed a bug that could cause a crash when using --comp-based-stats 0.
• Fixed a bug that could cause a crash for small input files in certain cases.
• Fixed a bug that could cause filtering hits for identity or range cover not to function correctly when using the tabular format without traceback being enabled.
• Added warning messages to recommend block size parameters based on system RAM.

DIAMOND v2.0.0

• Added the sensitivity modes --very-sensitive and --ultra-sensitive. Both modes are designed for finding distant hits of <40% identity with a sensitivity similar to BLAST, with the ultra-sensitive mode being the slightly more sensitive mode.
• The --block-size/-b parameter is set to 0.4 and the --index-chunks/-c parameter is set to 1 by default in the new sensitivity modes.
• Improved performance.
• Added the option --ext with possible values banded-fast and banded-slow to adjust band setup for Smith Waterman extensions (new default is banded-fast for the default and sensitive mode, and banded-slow otherwise).
• Added automatic disabling of alignment traceback if not required by the user-defined output fields in tabular output format.
• Changed the default value of the --max-hsps parameter (the maximum number of HSPs per target sequence to report for each query) to 1.
• Changed the default value of the --freq-sd parameter from 10 to 20 for the sensitive mode.
• Fixed a compiler error on FreeBSD.

DIAMOND v0.9.36

• Fixed a bug that could cause makedb to produce invalid database files when using taxonomy features.
• Fixed a bug that could cause a crash when running in query-indexed mode.

WARNING: This version contains a serious bug that can cause incomplete results in blastx mode. Using it is not recommended.

DIAMOND v0.9.35

• Fixed a bug in diamond view that would cause high memory usage and erroneous output.
• Reduced the use of temporary disk space.
• Fixed a database compatibility issue with big endian architectures.
• Fixed a bug that would cause a crash for query sequences shorter than 5 letters in blastx mode.
• Fixed a bug that would cause a crash when using a FASTA file as database parameter in blastx mode.
• Added support for the following new ranks in the NCBI taxonomy: biotype, clade, forma specialis, genotype, isolate, morph, pathogroup, serogroup, serotype, strain, subvariety.

WARNING: This version contains a serious bug that can cause incomplete results in blastx mode. Using it is not recommended.

DIAMOND v0.9.34

• Fixed a compiler error for native builds.
• Fixed a compiler error for GCC 4.8.
• Fixed a compiler error when support for SSSE3 was enabled without support for SSE4.1.
• Implemented asynchronous loading of seed hits.

WARNING: This version contains a serious bug that can cause incomplete results in blastx mode. Using it is not recommended.