.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.46.4.
.TH HHALIGN "1" "November 2014" "hhalign 2.0.16" "User Commands"
.SH NAME
hhalign \- align a query alignment/HMM to a template alignment/HMM
.SH SYNOPSIS
.B hhalign
\fI\,\-i query \/\fR[\fI\,\-t template\/\fR] [\fI\,options\/\fR]
.SH DESCRIPTION
HHalign version 2.0.16 (January 2013)
Align a query alignment/HMM to a template alignment/HMM by HMM\-HMM alignment
If only one alignment/HMM is given it is compared to itself and the best
off\-diagonal alignment plus all further non\-overlapping alignments above
significance threshold are shown.
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).
(C) Johannes Soeding, Michael Remmert, Andreas Biegert, Andreas Hauser
.TP
\fB\-i\fR <file>
input query alignment  (fasta/a2m/a3m) or HMM file (.hhm)
.TP
\fB\-t\fR <file>
input template alignment (fasta/a2m/a3m) or HMM file (.hhm)
.SS "Output options:"
.TP
\fB\-o\fR <file>
write output alignment to file
.TP
\fB\-ofas\fR <file>
write alignments in FASTA, A2M (\fB\-oa2m\fR) or A3M (\fB\-oa3m\fR) format
.TP
\fB\-Oa3m\fR <file>
write query alignment in a3m format to file (default=none)
.TP
\fB\-Aa3m\fR <file>
append query alignment in a3m format to file (default=none)
.TP
\fB\-atab\fR <file>
write alignment as a table (with posteriors) to file (default=none)
.HP
\fB\-index\fR <file> use given alignment to calculate Viterbi score (default=none)
.TP
\fB\-v\fR <int>
verbose mode: 0:no screen output  1:only warings  2: verbose
.TP
\fB\-seq\fR
[1,inf[ max. number of query/template sequences displayed  (def=1)
.TP
\fB\-nocons\fR
don't show consensus sequence in alignments (default=show)
.TP
\fB\-nopred\fR
don't show predicted 2ndary structure in alignments (default=show)
.TP
\fB\-nodssp\fR
don't show DSSP 2ndary structure in alignments (default=show)
.TP
\fB\-ssconf\fR
show confidences for predicted 2ndary structure in alignments
.TP
\fB\-aliw\fR int
number of columns per line in alignment list (def=80)
.TP
\fB\-P\fR <float>
for self\-comparison: max p\-value of alignments (def=0.001
.TP
\fB\-p\fR <float>
minimum probability in summary and alignment list (def=0)
.TP
\fB\-E\fR <float>
maximum E\-value in summary and alignment list (def=1E+06)
.TP
\fB\-Z\fR <int>
maximum number of lines in summary hit list (def=100)
.TP
\fB\-z\fR <int>
minimum number of lines in summary hit list (def=1)
.TP
\fB\-B\fR <int>
maximum number of alignments in alignment list (def=100)
.TP
\fB\-b\fR <int>
minimum number of alignments in alignment list (def=1)
.TP
\fB\-rank\fR int
specify rank of alignment to write with \fB\-Oa3m\fR or \fB\-Aa3m\fR option (default=1)
.SS "Filter input alignment (options can be combined):"
.TP
\fB\-id\fR
[0,100] maximum pairwise sequence identity (%) (def=90)
.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=100)
.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 "HMM\-HMM alignment options:"
.TP
\fB\-glob\fR/\-loc
global or local alignment mode (def=local)
.TP
\fB\-alt\fR <int>
show up to this number of alternative alignments (def=1)
.TP
\fB\-realign\fR
realign displayed hits with max. accuracy (MAC) algorithm
.TP
\fB\-norealign\fR
do NOT realign displayed hits with MAC algorithm (def=realign)
.TP
\fB\-mact\fR [0,1[
posterior probability threshold for MAC alignment (def=0.350)
A threshold value of 0.0 yields global alignments.
.TP
\fB\-sto\fR <int>
use global stochastic sampling algorithm to sample this many alignments
.HP
\fB\-excl\fR <range> exclude query positions from the alignment, e.g. '1\-33,97\-168'
.HP
\fB\-shift\fR [\-1,1] score offset (def=\-0.030)
.TP
\fB\-corr\fR [0,1]
weight of term for pair correlations (def=0.10)
.TP
\fB\-ssm\fR
0\-4     0:no ss scoring [default=2]
.IP
1:ss scoring after alignment
2:ss scoring during alignment
.TP
\fB\-ssw\fR
[0,1]   weight of ss score  (def=0.11)
.TP
\fB\-def\fR
read default options from ./.hhdefaults or <home>/.hhdefault.
.PP
Example: hhalign \fB\-i\fR T0187.a3m \fB\-t\fR d1hz4a_.hhm \fB\-png\fR T0187pdb.png
.SS "Output options:"
.TP
\fB\-o\fR <file>
write output alignment to file
.TP
\fB\-ofas\fR <file>
write alignments in FASTA, A2M (\fB\-oa2m\fR) or A3M (\fB\-oa3m\fR) format
.TP
\fB\-Oa3m\fR <file>
write query alignment in a3m format to file (default=none)
.TP
\fB\-Aa3m\fR <file>
append query alignment in a3m format to file (default=none)
.TP
\fB\-atab\fR <file>
write alignment as a table (with posteriors) to file (default=none)
.TP
\fB\-v\fR <int>
verbose mode: 0:no screen output  1:only warings  2: verbose
.TP
\fB\-seq\fR
[1,inf[  max. number of query/template sequences displayed  (def=1)
.TP
\fB\-nocons\fR
don't show consensus sequence in alignments (default=show)
.TP
\fB\-nopred\fR
don't show predicted 2ndary structure in alignments (default=show)
.TP
\fB\-nodssp\fR
don't show DSSP 2ndary structure in alignments (default=show)
.TP
\fB\-ssconf\fR
show confidences for predicted 2ndary structure in alignments
.TP
\fB\-aliw\fR int
number of columns per line in alignment list (def=80)
.TP
\fB\-P\fR <float>
for self\-comparison: max p\-value of alignments (def=0.001
.TP
\fB\-p\fR <float>
minimum probability in summary and alignment list (def=0)
.TP
\fB\-E\fR <float>
maximum E\-value in summary and alignment list (def=1E+06)
.TP
\fB\-Z\fR <int>
maximum number of lines in summary hit list (def=100)
.TP
\fB\-z\fR <int>
minimum number of lines in summary hit list (def=1)
.TP
\fB\-B\fR <int>
maximum number of alignments in alignment list (def=100)
.TP
\fB\-b\fR <int>
minimum number of alignments in alignment list (def=1)
.TP
\fB\-rank\fR int
specify rank of alignment to write with \fB\-Oa3m\fR or \fB\-Aa3m\fR option (default=1)
.TP
\fB\-tc\fR <file>
write a TCoffee library file for the pairwise comparison
.TP
\fB\-tct\fR [0,100]
min. probobability of residue pairs for TCoffee (def=5%)
.SS "Options to filter input alignment (options can be combined):"
.TP
\fB\-id\fR
[0,100]  maximum pairwise sequence identity (%) (def=90)
.TP
\fB\-diff\fR [0,inf[
filter most diverse set of sequences, keeping at least this
many sequences in each block of >50 columns (def=100)
.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 "HMM\-building options:"
.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
.TP
\fB\-tags\fR
do NOT neutralize His\-, C\-myc\-, FLAG\-tags, and
trypsin recognition sequence to background distribution
.SS "Pseudocount (pc) options:"
.TP
\fB\-pcm\fR
0\-2      position dependence of pc admixture 'tau' (pc mode, default=2)
.TP
0: no pseudo counts:
tau = 0
.TP
1: constant
tau = a
.IP
2: diversity\-dependent: tau = a/(1 + ((Neff[i]\-1)/b)^c)
(Neff[i]: number of effective seqs in local MSA around column i)
3: constant diversity pseudocounts
.TP
\fB\-pca\fR
[0,1]    overall pseudocount admixture (def=1.0)
.TP
\fB\-pcb\fR
[1,inf[  Neff threshold value for \fB\-pcm\fR 2 (def=1.5)
.TP
\fB\-pcc\fR
[0,3]    extinction exponent c for \fB\-pcm\fR 2 (def=1.0)
.TP
\fB\-pre_pca\fR [0,1]
PREFILTER pseudocount admixture (def=0.8)
.HP
\fB\-pre_pcb\fR [1,inf[ PREFILTER threshold for Neff (def=1.8)
.SS "Context\-specific pseudo\-counts:"
.TP
\fB\-nocontxt\fR
use substitution\-matrix instead of context\-specific pseudocounts
.HP
\fB\-contxt\fR <file> context file for computing context\-specific pseudocounts (default=./data/context_data.lib)
.TP
\fB\-cslib\fR
<file> column state file for fast database prefiltering (default=./data/cs219.lib)
.SS "Gap cost options:"
.TP
\fB\-gapb\fR [0,inf[
Transition pseudocount admixture (def=1.00)
.TP
\fB\-gapd\fR [0,inf[
Transition pseudocount admixture for open gap (default=0.15)
.TP
\fB\-gape\fR [0,1.5]
Transition pseudocount admixture for extend gap (def=1.00)
.TP
\fB\-gapf\fR ]0,inf]
factor to increase/reduce the gap open penalty for deletes (def=0.60)
.TP
\fB\-gapg\fR ]0,inf]
factor to increase/reduce the gap open penalty for inserts (def=0.60)
.TP
\fB\-gaph\fR ]0,inf]
factor to increase/reduce the gap extend penalty for deletes(def=0.60)
.TP
\fB\-gapi\fR ]0,inf]
factor to increase/reduce the gap extend penalty for inserts(def=0.60)
.TP
\fB\-egq\fR
[0,inf[  penalty (bits) for end gaps aligned to query residues (def=0.00)
.TP
\fB\-egt\fR
[0,inf[  penalty (bits) for end gaps aligned to template residues (def=0.00)
.SS "Alignment options:"
.TP
\fB\-glob\fR/\-loc
global or local alignment mode (def=global)
.TP
\fB\-mac\fR
use Maximum Accuracy (MAC) alignment instead of Viterbi
.TP
\fB\-mact\fR [0,1]
posterior prob threshold for MAC alignment (def=0.350)
.TP
\fB\-sto\fR <int>
use global stochastic sampling algorithm to sample this many alignments
.TP
\fB\-sc\fR
<int>    amino acid score         (tja: template HMM at column j) (def=1)
.TP
0
= log2 Sum(tja*qia/pa)   (pa: aa background frequencies)
.TP
1
= log2 Sum(tja*qia/pqa)  (pqa = 1/2*(pa+ta) )
.TP
2
= log2 Sum(tja*qia/ta)   (ta: av. aa freqs in template)
.TP
3
= log2 Sum(tja*qia/qa)   (qa: av. aa freqs in query)
.TP
\fB\-corr\fR [0,1]
weight of term for pair correlations (def=0.10)
.TP
\fB\-shift\fR [\-1,1]
score offset (def=\-0.030)
.TP
\fB\-r\fR
repeat identification: multiple hits not treated as independent
.TP
\fB\-ssm\fR
0\-2      0:no ss scoring [default=2]
.IP
1:ss scoring after alignment
2:ss scoring during alignment
.TP
\fB\-ssw\fR
[0,1]    weight of ss score compared to column score (def=0.11)
.TP
\fB\-ssa\fR
[0,1]    ss confusion matrix = (1\-ssa)*I + ssa*psipred\-confusion\-matrix [def=1.00)
.TP
\fB\-calm\fR 0\-3
empirical score calibration of 0:query 1:template 2:both (def=off)
.PP
Default options can be specified in './.hhdefaults' or '~/.hhdefaults'