Stockholm Tools

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 PhyloGram.pm and xrate).

Standalone Perl scripts:

• Visualization/colorization/pretty-printing of Stockholm alignments:
  • colorstock.pl - color alignment columns by stem in a Stockholm alignment of RNA secondary structures, using ANSI terminal color
  • (Deprecated) sscolor.pl and sscolorMult.pl - highlight covariant substitutions in a multiple alignment of RNA (written by Yuri Bendana)
• Conversions to & from common formats:
  • fasta2stockholm.pl - convert gapped FASTA alignments into Stockholm
  • stockholm2fasta.pl - convert Stockholm alignments into gapped FASTA alignment files, or ungapped FASTA sequence files
  • msf2stockholm.pl - convert MSF alignment format into Stockholm
• Conversions from various alignment database formats:
  • homstrad2stockholm.pl - convert the Homstrad Database multiple alignment format into Stockholm
  • optic2stockholm.pl - convert the Optic Database multiple alignment format into Stockholm
  • pandit2stockholm.pl - convert the Pandit Database format into Stockholm
• Conversions from various program output formats:
  • rnafold2stockholm.pl - convert the output of the VIENNA RNAfold program into Stockholm
  • clustal2stockholm.pl - convert the ALN output format of the CLUSTALW program into Stockholm
• Utilities:
  • constock.pl - given a database of Stockholm multiple alignments, all containing exactly the same sequences, return the "consensus" alignment (specifically, the subset of columns that maximises either the Sum Of Pairs Score or Total Column Score)
  • stockholm2ct.pl - extract secondary structures from a Stockholm alignment of RNA and write them as CT files (MFOLD)
  • splitstock.pl - split up a multiple alignment into lots of pairwise alignments, for purposes of training pairwise Stochastic Context Free Grammars
  • majorcons.pl - find majority-consensus annotation for an alignment whose rows are individually annotated
  • calc_ss_cons.pl - find consensus secondary structure annotation (conservative or liberal) for an alignment whose rows are individually annotated
  • stocktree.pl can be used to extract a Newick Format trees from a Stockholm Newick Format alignment
  • stockfilm.pl uses ANSI terminal color to render an animated impression of an MCMC sampling run in Stockholm Format

Perl modules in DART:

• Stockholm.pm and Stockholm::Database.pm - no-nonsense Perl modules for holding Stockholm alignments
  • See Stockholm perl module examples

Python modules in DART:

• Stk.py - generic Stockholm module

C++ utilities in DART:

• cmpalign.cc and cmpfold.cc - benchmarking tools for finding the homology overlap between Stockholm alignments (in terms of the Sum Of Pairs Score) as well as the overlap of basepair annotations in RNA secondary structures
• gc2gr-ss.cc - maps #=GC SS_cons lines (consensus secondary structure) to #=GR SS lines (by-sequence secondary structure)
• stockholm.h - the DART C++ Stockholm class. Related classes:
  • DartSrc:seq/alignment.h
  • DartSrc:seq/biosequence.h

Other Stockholm Format-related tools (not in DART)

Standalone Perl scripts:

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

Python modules:

• StkWeb.py - Stockholm module that outputs JSON format

hmmer/sreformat

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

• Belvu
• Jalview
• The MultAlign viewer in Chimera

Bioperl

Bioperl also has a Stockholm class.