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Synopsis

hhmake -i <file> -o <file> [options]

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Description

HHmake builds an HMM from an input alignment in A2M, A3M, or FASTA format, or converts between HMMER format (.hmm) and HHsearch format (.hhm).

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Required Parameters

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-i
file
required
Query alignment (A2M, A3M, or FASTA), or query HMM

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Output Options

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-o
file
HMM file to be written to (default: <infile.hhm>)
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-a
file
HMM file to be appended to
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-v
integer
default:"2"
Verbose mode:
  • 0: no screen output
  • 1: only warnings
  • 2: verbose
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-seq
integer
default:"10"
Max. number of query/template sequences displayed. Beware of overflows! All these sequences are stored in memory.
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-add_cons
flag
Make consensus sequence master sequence of query MSA
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-name
string
Use this name for HMM (default: use name of first sequence)

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Filter Query Multiple Sequence Alignment

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-id
integer
default:"90"
Maximum pairwise sequence identity (%) (range: 0-100)
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-diff
integer
default:"100"
Filter MSA by selecting most diverse set of sequences, keeping at least this many seqs in each MSA block of length 50
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-cov
integer
default:"0"
Minimum coverage with query (%) (range: 0-100)
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-qid
integer
default:"0"
Minimum sequence identity with query (%) (range: 0-100)
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-qsc
float
default:"-20.0"
Minimum score per column with query
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-neff
float
Target diversity of alignment (default: off, range: 1-inf)

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Input Alignment Format

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-M
string
default:"a2m"
Input alignment format:
  • a2m or a3m: upper case = Match; lower case = Insert; ’-’ = Delete; ’.’ = gaps aligned to inserts
  • first: 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

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Pseudocount Options

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Context-specific HHM pseudocounts

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-pc_hhm_contxt_mode
integer
default:"0"
Position dependence of pc admixture ‘tau’ (pc mode):
  • 0: no pseudo counts: tau = 0
  • 1: constant: tau = a
  • 2: diversity-dependent: tau = a/(1+((Neff[i]-1)/b)^c)
  • 3: CSBlast admixture: tau = a(1+b)/(Neff[i]+b)
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-pc_hhm_contxt_a
float
default:"0.9"
Overall pseudocount admixture (range: 0-1)
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-pc_hhm_contxt_b
float
default:"4.0"
Neff threshold value for mode 2 (range: 1-inf)
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-pc_hhm_contxt_c
float
default:"1.0"
Extinction exponent c for mode 2 (range: 0-3)

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Context-independent HHM pseudocounts

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-pc_hhm_nocontxt_mode
integer
default:"2"
Position dependence of pc admixture ‘tau’ (used for templates; used for query if contxt file is not available)
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-pc_hhm_nocontxt_a
float
default:"1.0"
Overall pseudocount admixture (range: 0-1)
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-pc_hhm_nocontxt_b
float
default:"1.5"
Neff threshold value for mode 2 (range: 1-inf)
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-pc_hhm_nocontxt_c
float
default:"1.0"
Extinction exponent c for mode 2 (range: 0-3)

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Context-specific pseudocounts

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-nocontxt
flag
Use substitution-matrix instead of context-specific pseudocounts
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-contxt
file
Context file for computing context-specific pseudocounts

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Other Options

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-maxseq
integer
default:"65535"
Max number of input rows
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-maxres
integer
default:"20000"
Max number of HMM columns

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Examples

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Build HMM from alignment

hhmake -i test.a3m -o stdout

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Build HMM with custom name

hhmake -i alignment.a3m -o model.hhm -name MyProtein

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Exit Codes

  • 0: Success
  • 1: File format error
  • 2: File access error
  • 3: Memory error
  • 4: Command line error

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See Also

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