Zoological Research Museum Alexander Koenig

is a member of Leibniz Association

Link to Leibniz Association


RNAsalsa adapts known strcuture information to the considered sequences in several steps. Conserved structure features are verified via primary sequence variation and the detection of consistent and compensatory substitutions, which requires internal alignment steps. Remaining highly variable sections, where conserved structures cannot be detected, are folded by minimizing free energy. The result is a complete individual secondary structure for each sequence. A final alignment is done by taking both structure and sequence information of each position into account. For further tree reconstruction analysis, a sequence alignment with a consensus structure allows the application of RNA substitution models in the conserved paired regions of the considered RNA genes. It is important to notice, that RNAsalsa uses structure information for adjusting and refining the sequence alignment and vice versa.


RNAsalsa is currently available in beta version 0.8.1

RNAsalsa _0.8.1.zip



Precompiled binaries for Win32 and Mac






 RNAsalsa uses so called constraint structures to adopt conserved structure elements. These constraints have to be provided in the dot-bracket format. The contraint file contains a few examples of ribosomal sequences with adjacent structure annotation, which can be used for RNAsalsa.


Manual v.1.4.2