Synopsis
Description
HHconsensus calculates the consensus sequence for an A3M/FASTA input file.Required Parameters
Query alignment (A2M, A3M, or FASTA), or query HMM
Output Options
Append consensus sequence in FASTA format (default: <infile.seq>)
Write alignment with consensus sequence in A3M format
Write alignment with consensus sequence in A3M format (same as -o)
Write alignment with consensus sequence in A2M format
Write alignment with consensus sequence in FASTA format
Verbose mode:
0: no screen output1: only warnings2: verbose
Filter Input Alignment
Maximum pairwise sequence identity (%) (range: 0-100)
Filter most diverse set of sequences, keeping at least this many sequences in each block of >50 columns
Minimum coverage with query (%) (range: 0-100)
Minimum sequence identity with query (%) (range: 0-100)
Minimum score per column with query
Input Alignment Format
Input alignment format:
a2mora3m: upper case = Match; lower case = Insert; ’-’ = Delete; ’.’ = gaps aligned to insertsfirst: FASTA format where columns with residue in 1st sequence are match states[0-100]: FASTA format where columns with fewer than X% gaps are match states
Other Options
Max number of input rows
Max number of HMM columns
Examples
Generate consensus sequence
Create consensus with alignment output
Exit Codes
0: Success1: File format error2: File access error3: Memory error4: Command line error
See Also
- hhmake - Build an HMM from an alignment
- hhfilter - Filter alignment
- A3M Format - Alignment format