v2.0.0 released

Benjamin Buchfink

Staff member
  • 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.