.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.8.
.TH HHCONSENSUS "1" "February 2019" "hhconsensus 3.0~beta3+dfsg" "User Commands"
.SH NAME
hhconsensus \- calculate the consensus sequence for an A3M/FASTA input file
.SH SYNOPSIS
.B hhconsensus
\fI\,\-i <file> \/\fR[\fI\,options\/\fR]
.SH DESCRIPTION
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).
.TP
\fB\-i\fR <file>
query alignment (A2M, A3M, or FASTA), or query HMM
.SS "Output options:"
.TP
\fB\-s\fR <file>
append consensus sequence in FASTA (default=<infile.seq>)
.TP
\fB\-o\fR <file>
write alignment with consensus sequence in A3M
.TP
\fB\-oa3m\fR <file>
same
.TP
\fB\-oa2m\fR <file>
write alignment with consensus sequence in A2M
.TP
\fB\-ofas\fR <file>
write alignment with consensus sequence in FASTA
.TP
\fB\-v\fR <int>
verbose mode: 0:no screen output  1:only warings  2: verbose
.SS "Filter input alignment (options can be combined):"
.TP
\fB\-id\fR
[0,100] maximum pairwise sequence identity (%) (def=100)
.HP
\fB\-diff\fR [0,inf[ filter most diverse set of sequences, keeping at least this
.IP
many sequences in each block of >50 columns (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)
.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:"
.HP
\fB\-maxres\fR <int> max number of HMM columns (def=20001)
.PP
Example: hhconsensus \fB\-i\fR stdin \fB\-s\fR stdout