hhconsensus − calculate the consensus sequence for an A3M/FASTA input file
hhconsensus −i <file> [options]
HHconsensus 3.0.0 (15−03−2015) Calculate the consensus sequence for an A3M/FASTA input file. (C) Johannes Soeding, Michael Remmert, 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) |
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−diff |
[0,inf[ filter most diverse set of sequences, keeping at least this
many sequences in each block of >50 columns (def=0)
−cov |
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[0,100] minimum coverage with query (%) (def=0) |
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−qid |
[0,100] minimum sequence identity with query (%) (def=0) |
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−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:
−maxres <int> max number of HMM columns (def=20001) |
Example: hhconsensus −i stdin −s stdout