anchor.diff:              }
           ///Perform a multiple sequence alignment of all the sequences in seqfile by aligning
           ///them individually to the profile HMM in hmmfile. The new alignment is output to
  -        ///stdout.
  +        ///stdout (when not specified otherwise).
           let runHMMalign (bcContext:BioContainer.BcContext) (opt:HMMalignParams list) =
               runHMMalignAsync bcContext opt
               |> Async.RunSynchronously
  
positive.code:  
              }
          
          let runHMMbuild (bcContext:BioContainer.BcContext) (opt:HMMbuildParams list) = 
              runHMMbuildAsync bcContext opt
              |> Async.RunSynchronously
  
negative.code: // adaped from the hmmer usage guide at http://eddylab.org/software/hmmer/Userguide.pdf
  // HMMER: biosequence analysis using profile hidden Markov models (http://hmmer.org/)
  
  ///HMMER - Biological sequence analysis using profile hidden Markov models
  ///Functions providing an API for the HMMER 3 biocontainer
  module HMMER =
  
      open BioContainer
  