diamond

Custom scoring matrices now also work when using the DAA format.

Added support for customizing the tabular output format. The format may now be specified similarly to BLAST:
diamond --outfmt 6 qseqid sseqid bitscore

This release adds support for custom scoring matrices. Syntax for using a custom matrix file:
diamond blastp --custom-matrix custom.mat --lambda 0.3 --K 0.1 --gapopen 10 --gapextend 2

Note that the statistical parameters Lambda and K have to be provided for your matrix. One way to compute these values is to use the FASTA suite. The file format of the matrix file also follows the format used by the FASTA suite.

Added a new command getseq that can be used to retrieve sequences from database files. Usage:
Print whole database in FASTA format: diamond getseq -d db
Print 3rd and 7th sequence in FASTA format: diamond getseq -d db --seq 3 7

Added a new alignment mode (option --more-sensitive) that provides some additional sensitivity compared to the sensitive mode.

With a new load balancing implementation, this release improves the performance particularly on systems with many cores and for longer sequences.

Fixed a crash and a compiler error on some systems.

Fixed a memory leak. Updating is recommended.

Fixed a compiler error on some older systems.

This release introduces a new database format that now allows to set the block size parameter for the alignment commands instead of the makedb command. This way the program's memory usage can be controlled more dynamically at runtime without database rebuilding.

Fixed a compiler error on some systems.

DIAMOND can now directly generate all of its output formats again - no need for the intermediate DAA file. Of course, the DAA format is still supported and should be used if you want to import the results into MEGAN.

This release comes with a substantial increase in performance and also improved accuracy of local alignments.

Fixed a compiler error on MAC.

By popular demand, DIAMOND now supports the BLAST XML output format (command line option -f xml). As these files can become very large, it is recommended to also activate compression of output files (option --compress 1).

Fixed a problem of the Windows version that could cause errors for larger files & fixed a problem that could cause very long runtimes for certain highly repetitive sequences.

Optimized performance.

This update fixes some problems that could cause too high memory usage in blastp mode and too long runtimes in certain cases.

This update improves the accuracy of local alignments and fixes a problem that could cause alignments to be missed sometimes.

Fixed a crash bug on Mac.