Stockholm format is an actively used text data format created in 1997.

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Example code from Wikipedia:

Feature   Description            Description
      -------   -----------            --------------
      RF        ReFerence annotation   Often the consensus RNA or protein sequence is used as a reference
                                       Any non-gap character (e.g. x's) can indicate consensus/conserved/match columns
                                       .'s or -'s indicate insert columns
                                       ~'s indicate unaligned insertions
                                       Upper and lower case can be used to discriminate strong and weakly conserved 
                                       residues respectively
      MM        Model Mask             Indicates which columns in an alignment should be masked, such
                                       that the emission probabilities for match states corresponding to
                                       those columns will be the background distribution.

Last updated February 11th, 2019