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:¶

-maxseq <int>

max number of input rows (def=65535)

-maxres <int> max number of HMM columns (def=20001)

Example: hhconsensus -i stdin -s stdout