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Builds a HMM profile from a multiple sequence alignment. The HMM profile is a statistical model which captures position-specific information about how conserved each column of the alignment is, and which residues are likely.

Parameters in GUI

ParameterDescriptionDefault value
Profile nameDescriptive name of the HMM profile. 
HMM strategySpecifies the kind of alignments you want to allow.hmmls
Calibrate profileEnables/disables optional profile calibration. An empirical HMM calibration costs time but it only has to be done once per model, and can greatly increase the sensitivity of a database search.True
Parallel calibrationNumber of parallel threads that the calibration will run in.1
Standard deviationStandard deviation of the synthetic sequence length. A positive number. Note that the Gaussian is left-truncated so that no sequences have lengths.200.0
Fixed length of samplesFixes the length of the random sequences to, where is a positive (and reasonably sized) integer. The default is instead to generate sequences with a variety of different lengths, controlled by a Gaussian (normal) distribution.0
Mean length of samplesMean length of the synthetic sequences, positive real number.325
Number of samplesNumber of synthetic sequences. If is less than about 1000, the fit to the EVD may fail Higher numbers of will give better determined EVD parameters. The default is 5000; it was empirically chosen as a tradeoff between accuracy and computation time.5000
Random seedThe random seed, where is a positive integer. The default is to use time() to generate a different seed for each run, which means that two different runs of hmmcalibrate on the same HMM will give slightly different results. You can use this option to generate reproducible results for different hmmcalibrate runs on the same HMM.0

Parameters in Workflow File

Type: hmm2-build

ParameterParameter in the GUIType
profile-nameProfile namestring
strategyHMM strategy


Available values are:

  • 0 - for hmms
  • 1 - for hmmls
  • 2 - for hmmfs
  • 3 - for hmmsw
calibrateCalibrate profileboolean
calibration-threadsParallel calibrationnumeric
deviationStandard deviationnumeric
fix-samples-lengthFixed length of samplesnumeric
mean-samples-lengthMean length of samplesnumeric
samples-numNumber of samplesnumeric
seedRandom seednumeric

Input/Output Ports

The element has 1 input port:

Name in GUI: Input MSA

Name in Workflow File: in-msa


Slot In GUISlot in Workflow FileType

And 1 output port:

Name in GUI: HMM profile

Name in Workflow File: out-hmm2


Slot In GUISlot in Workflow FileType
HMM profilehmm2-profilehmm2-profile
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