All tools rely upon RNA Framework. Make sure that the lib/ folder of RNA Framework is added to the $PERL5LIB environment variable:
$ export PERL5LIB=$PERL5LIB:/path/to/RNA/Frameworkor edit the relevant path in the individual scripts:
use lib "/path/to/RNAFramework/lib";cm-builder: automaGically builds structural alignments of RNAs and Infernal's CMs starting from a single sequence+structure and iteratively refining the model by searching against a database of related sequences
consensusFold: predicts a consensus secondary structure by aggregating multiple reactivity profiles using ViennaRNA's RNAalifold. This tool will become part of RNAFramework's rf-fold in future releases.
filterMM: post-processing of MM files prior to analysis with DRACO (filtering, extraction of target regions, etc.). This tool will become part of RNAFramework in future releases.
stockholmPolish: cleanup of Stockholm alignments generated by cm-builder
stockholm2html: structure-aware coloring of Stockholm alignments
transcriptome2genome: transcriptome-level to genome-level conversion of BED annotations