Multiple alignment programs

Thompson, J. D., Plewniak, F., and Poch, O. (1999). BAliBASE a benchmark alignment database for the evaluation of multiple alignment programs. Bioinformatics 15, 87-88. 

Multiple sequence alignment of orthologues and paralogues (either BLAST multiple alignment or (preferably) other multiple alignment program)... 

Several programs are now available that use multiple alignment of homologous proteins for prediction of secondary structure. One such program, called PHD, which was developed by Chris Sander and coworkers, EMBL, Heidelberg, has reached a mean accuracy of prediction of 72% for new structures. 

The third requirement is a scoring scheme to identify optimal dynamic programming alignments used in the above iterative multiple alignment... 

Another alternative is to compute an alignment of the predicted MFE structures. The RNAf or ester program is a new tool to perform such structure alignments and can also construct multiple alignments (in contrast to KNAdistance above). It is available as a web service at http / /bibiserv. techfak. uni-bielefeld.de/rna-forester/ although it does not yet offer multiple alignments. 

George, D. G., Multiple Sequence Alignment Program ALNED. NBRF, Washington, DC, 1988. 

Katoh K, Toh H (2008) Recent developments in the MAFFT multiple sequence alignment program. Brief Bioinform 9 286-298... 

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