Hhsuite

• hhalign(1) align a query alignment/HMM to a template alignment/HMM
• hhblits_omp(1) fast homology detection method to iteratively search a HMM database
• hhblits(1) fast homology detection method to iteratively search a HMM database
• hhconsensus(1) calculate the consensus sequence for an A3M/FASTA input file
• hhfilter(1) filter an alignment by maximum sequence identity of match states and minimum coverage
• hhmake(1) build an HMM from an input alignment or convert between HMMER format and HHsearch format
• hhsearch(1) search a database of HMMs with a query alignment or query HMM