Release MMseqs2 Release 7-4e23d · soedinglab/MMseqs2

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

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

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