Stockholm Tools

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Stockholm Format-related tools in DART

N.B. these lists include general-purpose Stockholm Format utilities and not the heavyweight probabilistic modeling tools in DART, many of which use Stockholm as their native alignment format (see in particular and xrate).

Standalone Perl scripts:

Perl modules in DART:

Python modules in DART:

  • - generic Stockholm module

C++ utilities in DART:

Other Stockholm Format-related tools (not in DART)

Standalone Perl scripts:

  • - split up a Stockholm alignment into several overlapping subalignments, using a sliding window
  • - add a New Hampshire format tree to every alignment in a Stockholm database, using the #=GF NH ... notation

Python modules:

  • - Stockholm module that outputs JSON format


The Squid library, distributed with the hmmer program for homology detection using profile HMMs, includes a program called sreformat that converts between various alignment formats, including Stockholm Format.

Alignment viewers


Bioperl also has a Stockholm class.