R-Coffee is a multiple sequence alignment package specificaly designed for RNA. Given a set of RNA sequences, R-Coffee generates a multiple sequence alignment using structural information. R-Coffee is included in the main distribution of T-Coffee (Version 5.60 or higher).
R-Coffee uses RNAlpfold to compute the secondary structure of the provided sequences. A modified version of T-Coffee is then used to compute the multiple sequence alignment having the best agreement with the sequences and the structures. R-Coffee can be combined with any existing sequence alignment method
R-Coffee: A Method for Multiple Alignment of Non-Coding RNA Andreas Wilm, Desmond G. Higgins & CÚdric Notredame.N.A.R. (in press)
Download the documentation from
R-Coffee is currently only available on the main server, but drop me a line if you want to set up a mirror.
Available R_coffee servers: