MMseqs2 Release 3-be8f6

Changes since 2-23394 Release

New Features

• Create simple workflows fasta/fastq in flat file out for clustering easy-cluster and searching easy-search
• Add a new clustering greedy incremental clustering algorithm to the clust module which needs less memory
• Make the new low memory clustering algorithm default if --cov-mode 1 is used in linclust and cluster
• Add alignall module for all-against-all alignments of e.g. clusters
• Improved Windows support
• filterdb learned new modes

Bug fixes

• Fix wrong merging code in linclust
• Fix e-value issues in target-split case
• Fix seg. fault in rescore diagonal if 'z' is used
• Fix seg. fault when using masking in kmermatcher
• Fix wrong filterdb default mode
• prefilter overestimated the required amount of memory and refused to run
• prefilter scores would saturate to early, now they have the full 2^16 range

Others

• Profile searches do create less high scoring false positive through better compositional bias correction and masking of low complexity regions of profiles
• Clustering supports now the whole 2^32 range instead the previously 2^31
• Speed up clustering when using --cov-mode 1
• Rework symlinks to the header databaes
• Support profiles on query and target side in result2profile