.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.3.
.TH HHFILTER "1" "August 2023" "hhfilter 3.3.0+ds" "User Commands"
.SH NAME
hhfilter \- filter an alignment by maximum sequence identity of match states and minimum coverage
.SH SYNOPSIS
.B hhfilter
\fI\,\-i infile \-o outfile \/\fR[\fI\,options\/\fR]
.SH DESCRIPTION
HHfilter 3.3.0
Filter an alignment by maximum pairwise sequence identity, minimum coverage,
minimum sequence identity, or score per column to the first (seed) sequence.n(c) The HH\-suite development team
Steinegger M, Meier M, Mirdita M, V??hringer H, Haunsberger S J, and S??ding J (2019)
HH\-suite3 for fast remote homology detection and deep protein annotation.
BMC Bioinformatics, doi:10.1186/s12859\-019\-3019\-7
.TP
\fB\-i\fR <file>
read input file in A3M/A2M or FASTA format
.TP
\fB\-o\fR <file>
write to output file in A3M format
.TP
\fB\-a\fR <file>
append to output file in A3M format
.SH OPTIONS
.TP
\fB\-v\fR <int>
verbose mode: 0:no screen output  1:only warings  2: verbose
.TP
\fB\-id\fR
[0,100]  maximum pairwise sequence identity (%) (def=90)
.TP
\fB\-diff\fR [0,inf[
filter MSA by selecting most diverse set of sequences, keeping
at least this many seqs in each MSA block of length 50 (def=0)
.TP
\fB\-cov\fR
[0,100]  minimum coverage with query (%) (def=0)
.TP
\fB\-qid\fR
[0,100]  minimum sequence identity with query (%) (def=0)
.TP
\fB\-qsc\fR
[0,100]  minimum score per column with query  (def=\-20.0)
.TP
\fB\-neff\fR [1,inf]
target diversity of alignment (default=off)
.SS "Input alignment format:"
.TP
\fB\-M\fR a2m
use A2M/A3M (default): upper case = Match; lower case = Insert;
\&'\-' = Delete; '.' = gaps aligned to inserts (may be omitted)
.TP
\fB\-M\fR first
use FASTA: columns with residue in 1st sequence are match states
.TP
\fB\-M\fR [0,100]
use FASTA: columns with fewer than X% gaps are match states
.SS "Other options:"
.TP
\fB\-maxseq\fR <int>
max number of input rows (def=65535)
.TP
\fB\-maxres\fR <int>
max number of HMM columns (def=20001)
.PP
Example: hhfilter \fB\-id\fR 50 \fB\-i\fR d1mvfd_.a2m \fB\-o\fR d1mvfd_.fil.a2m