Abstract
The study of RNA sequence structural alignments has become an important part of characterising noncoding RNAs. We developed RNApasta, a Java program with a graphical interface, to perform analysis and editing of RNA alignments. RNApasta can be used to generate statistics for modelling RNAs and to develop homogeneous subsets of alignments that contain variability. RNApasta includes several functions to characterise variation in stem and loop lengths, including phylogenetic analysis of this variation; as an example, we analyse variation in mir-31 pre-microRNA loop length variation, demonstrating that the sequences with longer loops had a single evolutionary origin.