@martin-steinegger martin-steinegger released this Nov 29, 2018 · 137 commits to master since this release

Assets 8

Changes since release 6-f5a1c

New features

  • Simplified taxonomy. We add tools the tools to create the taxonomical annotated database createtaxdb. It is possible to filter result databaese based on taxonomy with filtertaxdb and addtaxonomy to append taxonomy information to result databases
  • index (createindex) support for translated target databaes searches
  • add nucleotide search (experimental)
  • support NEON CPU architecture (experimental)
  • improve performance of prefilter if L2 is greater 256K
  • easy-search automatically computes backtrace if requested by --format-output
  • Create search-2m workflow, similiar to 2bLCA but without the LCA computation
  • We add a database preload mode. Database preload mode 0: auto, 1: fread, 2: mmap, 3: mmap+touch. The processing time per query with fread is 15% faster but the read in is slower. mmap is use for the MMseqs2 webserver, it enables instance searches if the database is already in memory, mmap+touch uses mmap an touches every page.
  • We add a new tool touchdb, it loads the database in memory. This can be useuful for "--db-load-mode 2.
  • add local hard disks support --local-tmp for MPI runs. This reduces pressure from the NFS
  • Introduce sortresult tool to sort an unordered sequence db (e.g. from mergeresult)
  • prefilter supports now indexes with k-mer ranges > 2^31
  • convertkb can read multiple files
  • speed up mmap memory touch function

breaking changes

  • new index version. Recomputation of old indexes in needed
  • --format-output is now comma separated
  • changed taxonomy database format, old taxonomy databaes are not supported anymore

default parameter change

  • extractorfs default is now --orf-start-mode 1. This is important for translated searches in organisms with introns.

Bug fixes

  • Fix wrong alignment positions for translated searches
  • Fix of by one error in extratalignedregion
  • Fix bug in NcbiTaxonomy tool
  • Fix e-value threshold if -e < --e-profile


  • Update to newest ALP version