Structured RNAs and the Accurate and Efficient Reconstruction of Deep Phylogenies

The software package RNAsalsa serves as a framework to perform improved RNA structure predictions as well as alignments of structural RNA sequences. It utilizes prior knowledge about structural patterns, adapted constraint directed thermodynamic folding algorithms, and comparative evidence methods. It automatically and simultaneously generates both highly corrected individual secondary structure predictions within a set of homologous RNA genes and a consensus structure for the set, and it takes then sequence and structure information into account as part of the alignment's scoring function. RNAsalsa uses structure information for adjusting and refining the sequence alignment and vice versa.
Phylogeny reconstruction tasks are the main group of applications for RNAsalsa; methods can be extended to RNA secondary structure, incorporating both the RNAsalsa derived (and mostly improved) models for the secondary structure elements of the RNA and also the alignment based on that extended structure information. Thus, it is possible to make the slower evolution of the structural features a reproducible source of information.
The current version of RNAsalsa is command line based and available either as source code, or as a pre-compiled executable for various common operating systems.
Current version:
RNAsalsa 0.8.1

[Download of source codes as .tar.gz archive]
[Download of source codes as ZIP file]
[Download of MS Windows (32bit) executable as ZIP file]
[The manual]

If you find this software useful for your research, please cite the following work:
Last modified: 2009-10-13 09:50:00 roman