Synopsis
Description
HHfilter filters an alignment by maximum pairwise sequence identity, minimum coverage, minimum sequence identity, or score per column to the first (seed) sequence.Required Parameters
Read input file in A3M/A2M or FASTA format
Write to output file in A3M format
Append to output file in A3M format
Filter Options
Verbose mode:
0: no screen output1: only warnings2: verbose
Maximum pairwise sequence identity (%) (range: 0-100)
Filter MSA by selecting most diverse set of sequences, keeping at least this many seqs in each MSA block of length 50
Minimum coverage with query (%) (range: 0-100)
Minimum sequence identity with query (%) (range: 0-100)
Minimum score per column with query
Target diversity of alignment (default: off, range: 1-inf)
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
Filter by sequence identity
Filter by coverage and identity
Exit Codes
0: Success1: File format error2: File access error3: Memory error4: Command line error
See Also
- hhmake - Build an HMM from an alignment
- hhconsensus - Calculate consensus sequence
- A3M Format - Alignment format