RILogo: visualizing RNA–RNA interactions

RIsearch: fast RNA–RNA interaction search using a simplified nearest-neighbor energy model

(2012) Anne Wenzel et al.   BIOINFORMATICS

R2R - software to speed the depiction of aesthetic consensus RNA secondary structures

(2011) Zasha Weinberg et al.   BMC BIOINFORMATICS

The PETfold and PETcofold web servers for intra- and intermolecular structures of multiple RNA sequences

(2011) S. E. Seemann et al.   NUCLEIC ACIDS RESEARCH

RNA–RNA interaction prediction based on multiple sequence alignments

(2010) Andrew X. Li et al.   BIOINFORMATICS

PETcofold: predicting conserved interactions and structures of two multiple alignments of RNA sequences

(2010) Stefan E. Seemann et al.   BIOINFORMATICS

Rfam: Wikipedia, clans and the "decimal" release

(2010) P. P. Gardner et al.   NUCLEIC ACIDS RESEARCH

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

Partition function and base pairing probabilities for RNA–RNA interaction prediction

(2009) Fenix W. D. Huang et al.   BIOINFORMATICS

VARNA: Interactive drawing and editing of the RNA secondary structure

(2009) Kévin Darty et al.   BIOINFORMATICS

De novo prediction of structured RNAs from genomic sequences

(2009) Jan Gorodkin et al.   TRENDS IN BIOTECHNOLOGY

RNAplex: a fast tool for RNA–RNA interaction search

(2008) Hakim Tafer et al.   BIOINFORMATICS

RNALogo: a new approach to display structural RNA alignment

(2008) Tzu-Hao Chang et al.   NUCLEIC ACIDS RESEARCH