MMseqs2 Release 6-f5a1c

Changes since release 5-9375b

New features

• Support user defined output format in convertalis.
• Add parameters for gap open and gap extension costs.
• Improve substitution matrix support. Letters of alphabet can now be chose freely.
• Add a few PAM matrices to the data folder. Chose them with the --sub-mat parameter.
• Support IUPAC codes in translated search.
• Add parameter to define a spaced k-mer pattern.
• Add a new module ungappedprefilter. It computes an optimal ungapped score using a vectorized algorithm.

Bug fixes

• Fix easy-linclust parameter parsing issue.
• Fix coverage filtering in align when the parameter --realign is set.
• Fix sequence identity computation in rescorediagonal --rescore-mode 2.
• Fix apply MPI support.
• Fix representative sequence output bug in result2repseq.
• Fix possible MPI issues in modules creating symlinks.
• Fix slightly wrong E-value computed in alignall module.

Known Issues

• easy-search output has only one column. Workaround: Add parameter --format-output "".