DIAMOND v0.9.13

• Fixed query positions in pairwise format for translated searches.
• Changed default behaviour of --max-hsps option to report an unlimited number of HSPs for a single query/subject pair. Previously, only the single best HSP for a query/subject pair was reported. Since several HSPs are not uncommon for multidomain proteins and may contain valuable information, the default behaviour has been changed to report any HSP if its query and subject ranges are not enveloped by a higher scoring HSP.

DIAMOND v0.9.12

• 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.

DIAMOND v0.9.11

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

DIAMOND v0.9.10

• Added --strand option to choose query strand for translated searches.
• Added dbinfo command to show information about a database file.

DIAMOND v0.9.9

• 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.

The taxonomic classification format is a new output format that does not print alignments, but only a taxonomic classification for each read using the LCA algorithm.

DIAMOND v0.9.8

• Fixed a compiler error.

DIAMOND v0.9.7

• Fixed compiler errors.
• Changed XML format for better compatibility with Blast2Go.

DIAMOND v0.9.6

• Fixed compiler errors.

DIAMOND v0.9.5

• Added support for named pipes.
• Added support for reading input files from stdin.
• Added more elaborate file I/O error messages.

DIAMOND v0.9.4

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