Provided by: hhsuite_2.0.16-1ubuntu1_amd64 bug

NAME

       hhalign - align a query alignment/HMM to a template alignment/HMM

SYNOPSIS

       hhalign -i query [-t template] [options]

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

       -i <file>
              input query alignment  (fasta/a2m/a3m) or HMM file (.hhm)

       -t <file>
              input template alignment (fasta/a2m/a3m) or HMM file (.hhm)

       -png <file>
              write dotplot into PNG-file (default=none)

   Output options:
       -o <file>
              write output alignment to file

       -ofas <file>
              write alignments in FASTA, A2M (-oa2m) or A3M (-oa3m) format

       -Oa3m <file>
              write query alignment in a3m format to file (default=none)

       -Aa3m <file>
              append query alignment in a3m format to file (default=none)

       -atab <file>
              write alignment as a table (with posteriors) to file (default=none)

       -index <file> use given alignment to calculate Viterbi score (default=none)

       -v <int>
              verbose mode: 0:no screen output  1:only warings  2: verbose

       -seq   [1,inf[ max. number of query/template sequences displayed  (def=1)

       -nocons
              don't show consensus sequence in alignments (default=show)

       -nopred
              don't show predicted 2ndary structure in alignments (default=show)

       -nodssp
              don't show DSSP 2ndary structure in alignments (default=show)

       -ssconf
              show confidences for predicted 2ndary structure in alignments

       -aliw int
              number of columns per line in alignment list (def=80)

       -P <float>
              for self-comparison: max p-value of alignments (def=0.001

       -p <float>
              minimum probability in summary and alignment list (def=0)

       -E <float>
              maximum E-value in summary and alignment list (def=1E+06)

       -Z <int>
              maximum number of lines in summary hit list (def=100)

       -z <int>
              minimum number of lines in summary hit list (def=1)

       -B <int>
              maximum number of alignments in alignment list (def=100)

       -b <int>
              minimum number of alignments in alignment list (def=1)

       -rank int
              specify rank of alignment to write with -Oa3m or -Aa3m option (default=1)

   Dotplot options:
       -dthr <float> probability/score threshold for dotplot (default=0.50)

       -dsca <int>
              if value <= 20: size of dot plot unit box in pixels if value > 20: maximum dot plot
              size in pixels (default=600)

       -dwin <int>
              average score over window [i-W..i+W] (for -norealign) (def=10)

       -dali <list>
              show alignments with indices in <list> in dot plot <list> = <index1>  ...  <indexN>
              or  <list> = all

   Filter input alignment (options can be combined):
       -id    [0,100] maximum pairwise sequence identity (%) (def=90)

       -diff [0,inf[ filter most diverse set of sequences, keeping at least this

              many sequences in each block of >50 columns (def=100)

       -cov   [0,100] minimum coverage with query (%) (def=0)

       -qid   [0,100] minimum sequence identity with query (%) (def=0)

       -qsc   [0,100] minimum score per column with query  (def=-20.0)

   Input alignment format:
       -M a2m use A2M/A3M (default): upper case = Match; lower case = Insert; '-' = Delete; '.' =
              gaps aligned to inserts (may be omitted)

       -M first
              use FASTA: columns with residue in 1st sequence are match states

       -M [0,100]
              use FASTA: columns with fewer than X% gaps are match states

   HMM-HMM alignment options:
       -glob/-loc
              global or local alignment mode (def=local)

       -alt <int>
              show up to this number of alternative alignments (def=1)

       -realign
              realign displayed hits with max. accuracy (MAC) algorithm

       -norealign
              do NOT realign displayed hits with MAC algorithm (def=realign)

       -mact [0,1[
              posterior probability threshold for MAC alignment (def=0.350) A threshold value  of
              0.0 yields global alignments.

       -sto <int>
              use global stochastic sampling algorithm to sample this many alignments

       -excl <range> exclude query positions from the alignment, e.g. '1-33,97-168'

       -shift [-1,1] score offset (def=-0.030)

       -corr [0,1]
              weight of term for pair correlations (def=0.10)

       -ssm   0-4     0:no ss scoring [default=2]

              1:ss scoring after alignment 2:ss scoring during alignment

       -ssw   [0,1]   weight of ss score  (def=0.11)

       -def   read default options from ./.hhdefaults or <home>/.hhdefault.

       Example: hhalign -i T0187.a3m -t d1hz4a_.hhm -png T0187pdb.png

   Output options:
       -o <file>
              write output alignment to file

       -ofas <file>
              write alignments in FASTA, A2M (-oa2m) or A3M (-oa3m) format

       -Oa3m <file>
              write query alignment in a3m format to file (default=none)

       -Aa3m <file>
              append query alignment in a3m format to file (default=none)

       -atab <file>
              write alignment as a table (with posteriors) to file (default=none)

       -v <int>
              verbose mode: 0:no screen output  1:only warings  2: verbose

       -seq   [1,inf[  max. number of query/template sequences displayed  (def=1)

       -nocons
              don't show consensus sequence in alignments (default=show)

       -nopred
              don't show predicted 2ndary structure in alignments (default=show)

       -nodssp
              don't show DSSP 2ndary structure in alignments (default=show)

       -ssconf
              show confidences for predicted 2ndary structure in alignments

       -aliw int
              number of columns per line in alignment list (def=80)

       -P <float>
              for self-comparison: max p-value of alignments (def=0.001

       -p <float>
              minimum probability in summary and alignment list (def=0)

       -E <float>
              maximum E-value in summary and alignment list (def=1E+06)

       -Z <int>
              maximum number of lines in summary hit list (def=100)

       -z <int>
              minimum number of lines in summary hit list (def=1)

       -B <int>
              maximum number of alignments in alignment list (def=100)

       -b <int>
              minimum number of alignments in alignment list (def=1)

       -rank int
              specify rank of alignment to write with -Oa3m or -Aa3m option (default=1)

       -tc <file>
              write a TCoffee library file for the pairwise comparison

       -tct [0,100]
              min. probobability of residue pairs for TCoffee (def=5%)

   Dotplot options:
       -dwin int
              average score in dotplot over window [i-W..i+W] (def=10)

       -dthr float
              score threshold for dotplot (default=0.50)

       -dsca int
              size of dot plot box in pixels  (default=600)

       -dali <list>
              show  alignments  with indices in <list> in dot plot <list> = <index1> ... <indexN>
              or  <list> = all

       -dmap <file>
              print list of coordinates in png plot

   Options to filter input alignment (options can be combined):
       -id    [0,100]  maximum pairwise sequence identity (%) (def=90)

       -diff [0,inf[
              filter most diverse set of sequences, keeping at least this many sequences in  each
              block of >50 columns (def=100)

       -cov   [0,100]  minimum coverage with query (%) (def=0)

       -qid   [0,100]  minimum sequence identity with query (%) (def=0)

       -qsc   [0,100]  minimum score per column with query  (def=-20.0)

   HMM-building options:
       -M a2m use A2M/A3M (default): upper case = Match; lower case = Insert; '-' = Delete; '.' =
              gaps aligned to inserts (may be omitted)

       -M first
              use FASTA: columns with residue in 1st sequence are match states

       -M [0,100]
              use FASTA: columns with fewer than X% gaps are match states

       -tags  do NOT neutralize His-, C-myc-, FLAG-tags,  and  trypsin  recognition  sequence  to
              background distribution

   Pseudocount (pc) options:
       -pcm   0-2      position dependence of pc admixture 'tau' (pc mode, default=2)

       0: no pseudo counts:
              tau = 0

       1: constant
              tau = a

              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

       -pca   [0,1]    overall pseudocount admixture (def=1.0)

       -pcb   [1,inf[  Neff threshold value for -pcm 2 (def=1.5)

       -pcc   [0,3]    extinction exponent c for -pcm 2 (def=1.0)

       -pre_pca [0,1]
              PREFILTER pseudocount admixture (def=0.8)

       -pre_pcb [1,inf[ PREFILTER threshold for Neff (def=1.8)

   Context-specific pseudo-counts:
       -nocontxt
              use substitution-matrix instead of context-specific pseudocounts

       -contxt   <file>   context    file    for    computing    context-specific    pseudocounts
              (default=debian/tmp/usr/share/hhsuite/data/context_data.lib)

       -cslib
              <file>     column     state     file     for     fast     database     prefiltering
              (default=debian/tmp/usr/share/hhsuite/data/cs219.lib)

   Gap cost options:
       -gapb [0,inf[
              Transition pseudocount admixture (def=1.00)

       -gapd [0,inf[
              Transition pseudocount admixture for open gap (default=0.15)

       -gape [0,1.5]
              Transition pseudocount admixture for extend gap (def=1.00)

       -gapf ]0,inf]
              factor to increase/reduce the gap open penalty for deletes (def=0.60)

       -gapg ]0,inf]
              factor to increase/reduce the gap open penalty for inserts (def=0.60)

       -gaph ]0,inf]
              factor to increase/reduce the gap extend penalty for deletes(def=0.60)

       -gapi ]0,inf]
              factor to increase/reduce the gap extend penalty for inserts(def=0.60)

       -egq   [0,inf[  penalty (bits) for end gaps aligned to query residues (def=0.00)

       -egt   [0,inf[  penalty (bits) for end gaps aligned to template residues (def=0.00)

   Alignment options:
       -glob/-loc
              global or local alignment mode (def=global)

       -mac   use Maximum Accuracy (MAC) alignment instead of Viterbi

       -mact [0,1]
              posterior prob threshold for MAC alignment (def=0.350)

       -sto <int>
              use global stochastic sampling algorithm to sample this many alignments

       -sc    <int>    amino acid score         (tja: template HMM at column j) (def=1)

       0      = log2 Sum(tja*qia/pa)   (pa: aa background frequencies)

       1      = log2 Sum(tja*qia/pqa)  (pqa = 1/2*(pa+ta) )

       2      = log2 Sum(tja*qia/ta)   (ta: av. aa freqs in template)

       3      = log2 Sum(tja*qia/qa)   (qa: av. aa freqs in query)

       -corr [0,1]
              weight of term for pair correlations (def=0.10)

       -shift [-1,1]
              score offset (def=-0.030)

       -r     repeat identification: multiple hits not treated as independent

       -ssm   0-2      0:no ss scoring [default=2]

              1:ss scoring after alignment 2:ss scoring during alignment

       -ssw   [0,1]    weight of ss score compared to column score (def=0.11)

       -ssa   [0,1]    ss confusion matrix = (1-ssa)*I + ssa*psipred-confusion-matrix [def=1.00)

       -calm 0-3
              empirical score calibration of 0:query 1:template 2:both (def=off)

       Default options can be specified in './.hhdefaults' or '~/.hhdefaults'