Query: hhconsensus
OS: debian
Section: 1
Format: Original Unix Latex Style Formatted with HTML and a Horizontal Scroll Bar
HHCONSENSUS(1) User Commands HHCONSENSUS(1)NAMEhhconsensus - calculate the consensus sequence for an A3M/FASTA input fileSYNOPSIShhconsensus -i <file> [options]DESCRIPTIONHHconsensus version 2.0.15 (June 2012) Calculate the consensus sequence for an A3M/FASTA input file. (C) Johannes Soeding, Michael Rem- mert, Andreas Biegert, Andreas Hauser Remmert M, Biegert A, Hauser A, and Soding J. HHblits: Lightning-fast iterative protein sequence searching by HMM-HMM alignment. Nat. Methods 9:173-175 (2011). -i <file> query alignment (A2M, A3M, or FASTA), or query HMM Output options: -s <file> append consensus sequence in FASTA (default=<infile.seq>) -o <file> write alignment with consensus sequence in A3M -oa3m <file> same -oa2m <file> write alignment with consensus sequence in A2M -ofas <file> write alignment with consensus sequence in FASTA -v <int> verbose mode: 0:no screen output 1:only warings 2: verbose Filter input alignment (options can be combined): -id [0,100] maximum pairwise sequence identity (%) (def=100) -diff [0,inf[ filter most diverse set of sequences, keeping at least this many sequences in each block of >50 columns (def=0) -cov [0,100] minimum coverage with query (%) (def=0) -qid [0,100] minimum sequence identity with query (%) (def=0) -qsc [0,100] minimum score per column with query (def=-20.0) Input alignment format: -M a2m use A2M/A3M (default): upper case = Match; lower case = Insert; '-' = Delete; '.' = gaps aligned to inserts (may be omitted) -M first use FASTA: columns with residue in 1st sequence are match states -M [0,100] use FASTA: columns with fewer than X% gaps are match states Other options: -addss add predicted secondary structure information from PSIPRED Example: hhconsensus -i stdin -s stdout hhconsensus 2.0.15 June 2012 HHCONSENSUS(1)