[2.0.7]
- Added support for computing full-matrix instead of banded Smith Waterman extensions
  (command line option `--ext full`).
- Added support for the new `prot.accession2taxid.FULL.gz` taxonomy mapping file from
  NCBI.
- Added the option `--gapped-filter-evalue` to set the e-value threshold of the gapped
  filter heuristic.
- Added setting the scores of the mask letter according to BLAST rules when a
  compositionally adjusted matrix is used.
- Changed formatting of e-values to print two decimals instead of one.
- Added the output field `qseq_translated` to print the translation of the aligned part
  of the query sequence.
- Added support for providing two input files to `--query/-q` when running alignment
  in blastx mode.
- Added the output field `full_qseq_mate` to print the sequence of the query's mate
  (enabled when using two query files in blastx mode).
- Fixed a bug that could cause a crash in blastx mode for very long queries.

[2.0.6]
- 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.

[2.0.5]
- Fixed an issue that could cause high memory use in frameshift alignment mode.

[2.0.4]
- 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.

[2.0.3]
- 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.

[2.0.2]
- 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.

[2.0.1]
- Added feature for using the tool in a distributed computing environment.
- Fixed an issue that could cause increased memory usage and runtimes for very long queries.
- 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.

[2.0.0]
- Added the sensitivity modes `--very-sensitive` and `--ultra-sensitive`.
- 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 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.

[0.9.36]
- 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.

[0.9.35]
- 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.

[0.9.34]
- 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.

[0.9.33]
- Improved performance and sensitivity.
- Increased use of temporary disk space.
- Implemented support for the AVX2 instruction set.
- Fixed a bug on big-endian architectures.
- Fixed bugs for compilers with unsigned char.
- Fixed compiler errors for generic builds.
- Added compatibility of database files between little and big endian architectures.
- Fixed various issues related to `Illegal instruction` errors on macOS.
- Added option `--file-buffer-size` to set the size of the I/O buffers and set the default value to 64 MB.

[0.9.32]
- Fixed a bug that would generate an incorrect count of positive scoring letters in all output formats.
- Fixed a compiler error on macOS.
- Fixed an `illegal instruction` error on macOS.

[0.9.31]
- Improved performance.
- Composition based statistics use integer scoring.
- Option `--quiet` will suppress startup message.
- Added output field `scovhsp` to print the subject coverage per HSP to the tabular format.
- Added option `--culling-overlap` to set the minimum overlap with a higher scoring hit for a hit to be deleted and changed the
  default value from 90% to 50%.
- Added command `diamond test` to run a series of regression tests.
- Fixed an off-by-one error of the query end position in the XML output format.
- (Update 2020/06/08) Due to a bug, since this version DAA files are not backward compatible with previous versions when using frameshift alignment (option `-F`).

[0.9.30]
- Added support for output field `cigar` to the tabular format.
- Changed the maximum repeat period to 50 for tantan masking.
- Changed the tantan masking to ungapped mode.
- Improved the performance of repeat masking.
- Added output fields sskingdoms, skingdoms, and sphylums to print subject super kingdoms, subject kingdoms, and subject phylums.

[0.9.29]
- Fixed a bug that could cause taxonomy features to function incorrectly for databases created by versions 0.9.27 and 0.9.28.

[0.9.28]
- Fixed a bug that could cause alignment score overflows for scores > 65535 in frameshift alignment mode.
- Fixed a clang compiler error.

[0.9.27]
- Improved performance of the seed matching stage.
- Seed frequency counts are computed based on hit seeds.
- Added option `--taxon-exclude` to exclude list of taxon ids from search.
- Compiling from source will no longer perform a native build. Instead, a portable binary that contains code paths
  for multiple architectures will be produced, with dispatch logic that is invoked at runtime.

[0.9.26]
- Fixed a bug that could cause undefined behaviour when using a database file of format version < 2.
- Fixed a compiler error when compiled as generic C++.
- Program will no longer terminate with an error if unlink system call fails.
- Added option `--tantan-minMaskProb` to set minimum repeat probability for tantan masking and changed the default value to 0.9.
- Added option `--tantan-maxRepeatOffset` to set maximum tandem repeat period to consider and changed the default value to 15.
- Added option `--tantan-ungapped` to use tantan in ungapped mode and changed the default to gapped mode.
- Changed score matrix lambda calculation for tantan masking.
- Reference masking is recomputed during alignment runs.

[0.9.25]
- Added support for the `sscinames` output field to print subject scientific names to the tabular output format.
- Fixed a compiler error for GCC 8.2.
- Added option `--stop-match-score` to set the match score of stop codons.
- Fixed a bug that caused the `qqual` output field to not be correctly clipped to the aligned part of the query.
- Added output fields `qseq_gapped` and `sseq_gapped` to the tabular format.
- Raised compiler requirement to GCC 4.8.
- Fixed a bug that caused the final sequence positions to not be printed in the pairwise format.
- Allow using `--min-score` instead of `--top` for the LCA computation of the taxonomy output format.
- Reduced the number of temporary files.
- Added output field `qstrand` to the tabular format.
- Database format version changed to 3.
- Fixed a bug in the `--range-culling` mode that could cause undefined behaviour.

[0.9.24]
- Fixed a compiler error on macOS.
- Added --header option to output header for tabular output format.
- The quality string output in tabular format (qqual field) is clipped to the aligned part of the query.
- Print '*' as quality string if quality values are not available in tabular output format.
- Added field 'full_qqual' to print unclipped query quality values to the tabular format.
- Added field 'full_qseq' to print unclipped query sequence to the tabular format.
- Added support for using the hyphen character '-' to denote the standard input for input file parameters.
- Status messages are written to stderr.
- Fixed a bug that could incorrectly report queries as unaligned in the output of the --un option.
- Added option '--al' to write aligned queries to file.
- Added options '--alfmt' and '--unfmt' to set the format of the aligned/unaligned query file (supported values: fasta, fastq).

[0.9.23]
- Fixed an issue that could cause too high memory usage.
- Added output field 'qqual' to print query FASTQ quality values to the tabular format.
- Changed license to GPL.
- Raised compiler requirement to GCC 4.6.
- Added option to use the DAA output format for diamond view.
- Added support for using a FASTA file as the --db parameter in alignment workflows.
- Added CL (command line) and VN (version) fields to the @PG SAM format header line.
- Fixed a performance issue for very long query sequences.
- Added shortcut --long-reads for --range-culling --top 10 -F 15.

[0.9.22]
- Added output field full_sseq to tabular output format.
- Database sequences that exceed the maximum accession length will no longer cause an error.
- Added support for PAF output format.
- Optimized performance of database taxonomy filtering.

[0.9.21]
- Fixed compiler errors on some systems.

[0.9.20]
- Added Bioconda installation instructions to manual.
- Added official docker release: https://hub.docker.com/r/buchfink/diamond/
- Fixed a bug that could cause corrupted output if compression was activated.
- Fixed an issue that could cause high memory usage by automatic use of the query-indexed algorithm.

[0.9.19]
- Fixed a bug in the --un function to write unaligned reads.
- Fixed an issue in the LCA algorithm that could cause an assignment to a higher node.
- --taxonmap and --taxonnodes parameters now apply exclusively to the makedb command.
- Added option --taxonlist to filter searches by subject taxonomic id.
- Changed database format; rebuilding is required.

[0.9.18]
- Optimized output writing performance.
- Fixed a bug in the XML output format.

[0.9.17]
- Fixed a compiler error on FreeBSD.
- Added option --range-culling.
- Fixed escape sequences in XML output.

[0.9.16]
- Fixed a bug that caused an error for non-SSSE3 builds.

[0.9.15]
- Improved performance of frameshift alignment mode.

[0.9.14]
- Added support for frameshift alignments.

[0.9.13]
- Fixed query positions in pairwise format for translated searches.
- Changed default behaviour of --max-hsps option to report unlimited number of HSPs.

[0.9.12]
- Fixed dbinfo command to be able to read older database formats.
- Adjusted XML format for better compatibility with Blast2Go.
- Fixed a potential error when running multiple instances of Diamond.

[0.9.11]
- Added option --xml-blord-format for alternative-style XML format.
- Fixed a bug that could cause a crash when writing compressed output files.

[0.9.10]
- added --strand option to choose query strand
- added dbinfo command

[0.9.9]
- Added taxonomic classification format.
- Fixed a bug in getseq printing masked residues.
- Fixed parsing of UniRef100_ sequence id prefixes.
- Added support for using the staxids output field in diamond view.

[0.9.8]
- Fixed a compiler error.

[0.9.7]
- Fixed compiler errors.
- Changed XML format to print accessions in the Hit_id and Hit_accession fields.

[0.9.6]
- Fixed compiler errors.

[0.9.5]
- Added support for named pipes.
- Added support for reading input files from stdin.
- Added more elaborate file I/O error messages.

[0.9.4]
- Improved performance.
- Fixed a bug in the query-indexed algorithm.
- Empty sequences are ignored instead of generating an error.

[0.9.3]
- Fixed a bug that could cause hanging.
- Fixed a bug that could cause an error when using the staxids output field and the --unal option.

[0.9.2]
- Fixed a compiler error.
- Improved performance for very small query files.

[0.9.1]
- fixed a performance issue

[0.9.0]
- improved performance
- improved support for alignments with long gaps
- removed SEG masking
- added low complexity masking using tantan
- changed license to AGPL

[0.8.38]
- fixed std::exception error messages
- fixed sequence titles in XML format
- XML and pairwise format contain full length titles by default

[0.8.37]
- fixed a bug that would cause an error message for empty DAA files
- all scoring matrices use the respective default gap penalties from BLAST
- added check for SSSE3 instruction set
- added diamond-sse2 to the binary package
- added staxids field to the tabular format

[0.8.36]
- fixed a compiler error

[0.8.35]
- added a check to detect incomplete database files
- database files will be deleted in case database building fails
- fixed a compiler error on 32 bit systems

[0.8.34]
- fixed a compiler error

[0.8.33]
- modified option --no-self-hits to also require matching sequence titles for filtering of a self hit
- fixed a bug that could cause a crash in the `joining output blocks` stage

[0.8.32]
- improved speed and sensitivity
- fixed an issue that could cause too high memory usage in certain cases

[0.8.31]
- renamed option --run-len to --min-orf
- added compositional score adjustments (option --comp-based-stats (0,1), enabled by default)
- removed --single-domain option and replaced by --max-hsps
- added option --no-self-hits

[0.8.30]
- slightly improved sensitivity
- added option to report unaligned queries (--unal)
- pairwise, XML and SAM format will report unaligned queries by default
- added option to filter alignments by subject cover (--subject-cover)

[0.8.29]
- fixed an issue that could cause a crash when using view on incomplete DAA files

[0.8.28]
- slightly improved sensitivity
- added support for the BLAST pairwise format (option -f 0)

[0.8.27]
- added support for gzip compressed files containing multiple gzip streams

[0.8.26]
- fixed a compiler error
- now compiles as generic C++ code without SSE being available
- added option to write unaligned queries to file (--un)

[0.8.25]
- fixed a bug with the qseq field in the blast tabular format
- added qtitle and btop fields to the blast tabular format
- fixed a bug that could cause a crash when passing a nonexistant input file
- fixed an issue that could cause unexpectedly long runtimes in certain cases

[0.8.24]
- error messages when reading sequence files include line numbers

[0.8.23]
- added option to change the genetic code used for translation in blastx mode

[0.8.22]
- the Hit_id and Hit_accession fields are now filled for the BLAST XML format

[0.8.21]
- fixed an error of 'diamond view' when using a custom scoring matrix

[0.8.20]
- added support for customizing the BLAST tabular output format

[0.8.19]
- ungapped xdrop score and ungapped and gapped filter scores are now set in bits
- added support for custom scoring matrices

[0.8.18]
- fixed a crash bug
- implemented getseq command to retrieve sequences from database files

[0.8.17]
- slightly improved sensitivity of fast and sensitive mode
- added new alignment mode (option --more-sensitive)
- the scoring matrix parameter will accept upper case spelling

[0.8.16]
- optimized performance

[0.8.15]
- fixed a compiler error on Mac
- fixed a crash on some systems

[0.8.14]
- fixed a memory leak

[0.8.13]
- fixed a compiler error for GCC 4.1 and 4.2

[0.8.12]
- changed database format
- block size parameter is set only for the alignment commands
- the program will accept databases created by later versions if the format is compatible
- improved sensitivity of sensitive mode with some loss in performance

[0.8.11]
- fixed a compiler error

[0.8.10]
- added option to directly generate all output formats
- fixed some GCC 6.1 compiler errors

[0.8.9]
- optimized performance
- improved local alignment accuracy
- fixed some fields in the XML format

[0.8.8]
- fixed a clang compiler error

[0.8.7]
- added support for BLAST XML format
- fixed the gzip compressed output option

[0.8.6]
- fixed a problem of the Windows version that could cause errors for larger files
- optimized performance

[0.8.5]
- optimized performance

[0.8.4]
- fixed a problem that could cause very long runtimes for highly repetitive sequences
- optimized performance
- fixed a bug that could cause too high memory usage in blastp mode

[0.8.3]
- fixed a problem that could sometimes cause alignments to be missed
- suppressed reporting of alignments that are enveloped by better alignments

[0.8.2]
- use parameter -k0 to report unlimited number of alignments
- fixed a crash bug on Mac OS X
- fixed a crash when view was used with terminal output

[0.8.1]
- added option to disable auto appending of DAA and DMND file extensions (--no-auto-append)
- fixed some compiler errors for GCC 4.6

[0.8.0]
- fixed a bug that would sometimes cause alignments to be missed
- fixed a bug that would cause alignments on the reverse strand to be missed in blastx mode
- temporary directory now defaults to output directory
- removed dependency on Boost
- fixed a bug that would cause stop codons to be translated into 'X'

[0.7.12]
- fixed header string in SAM output to correctly identify the blastp alignment mode
- added option to filter alignments for a given query cover (option --query-cover)
- added option to print full subject titles in output files (option --salltitles)

[0.7.11]
- added --version switch
- added static build option for CMake build
- fixed a bug that would cause a return code of 1 without an error

[0.7.10]
- --log option works on OS X
- added option to set effective database size (--dbsize)
- added CMake build option
- fixed a Clang compiler warning
- dash characters (-) are ignored (treated as X) in protein sequences

[0.7.9]
- added --single-domain option
- fixed a bug that could cause the program not to use all available threads
- optimized performance

[0.7.8]
- fixed a bug that could produce an incorrect sort order of HSPs

[0.7.7]
- fixed a number formatting error in the SAM output format

[0.7.6]
- fixed a formatting error in CIGAR strings

[0.7.5]
- fixed a compiler error for Clang
- compiles on OS X
- fixed a bug that would not produce the correct sort order for HSPs with e-value 0
- option --run-len defaults to 1 for sequences shorter than 30 letters

[0.7.4]
- removed OpenMP dependency
- using explicit Makefile instead of autoconf
- file extensions can be named explicitly for DAA and database files
- HSPs are grouped by target sequence
- fixed a bug that could produce incorrect output for view
- fixed a bug that could report an incorrect number of alignments
- fixed a compiler error for GCC 4.1.2

[0.7.3]
- changed database format (makedb required)
- optimized multithreading load balancing
- removed a non-determinism in alignment computation
- IUPAC nucleotide ambiguity codes in DNA sequences are accepted and converted into N's
- SEG masking is disabled by default for blastp mode
- fixed a memory leak
- reduced database file sizes

[0.7.2]
- fixed a bug that could create invalid DAA files when using the --id option
- added integrity check of DAA files to view command
- fixed a bug that could cause segmentation fault or file seek errors

[0.7.1]
- fixed a race condition for opening temporary files
- temporary files are deleted on ungraceful termination of the program
- blank lines in FASTA files are tolerated
- fixed a compiler error for GCC 4.4.7
- view command can write to standard output

[0.7.0]
- introduced DAA format
- reduced usage of temporary disk space and memory
- fixed a compiler error for GCC 4.1.2
- fixed a bug that could cause the program to hang when running out of temporary space or memory
- added --forwardonly option to view command