|Performance comparison on BAliBASE 3.0|
|Ranking of MSA tools on BAliBASE|
|ProGraphMSA D (noCS)||0.313**||0.63*||0.328||0.321||0.41***|
Displayed are the average true column scores (CS) for the truncated (BBS*) alignments of the RV11, RV12, RV20, and RV30 sets as well as the average over all these sets. Apart from a few exceptions the listing order of the tools implies significantly improving performance. Between each pair of subsequent scores for two different tools we perform a Wilcoxon signed-rank test. Stars indicate a significant difference at a p<0.05,p<0.01,p<0.001 level, respectively. In particular, the use of context-sensitive profiles significantly improves ProGraphMSA D's alignments, whereas our optimized version of ProGraphMSA significantly outperforms ClustalW (p=0.0024) but does scarcely not outperform Muscle without refinement (p=0.067) at the defined significance level.
Szalkowski BMC Bioinformatics 2012 13:129 doi:10.1186/1471-2105-13-129