This page provides supplementary materials for paper "MANGO: a new approach to multiple sequence alignment". It lists alignment results for MSA software: ClustalW, MUSCLE, MAFFT, Dialign, DIALIGN-T, T-Coffee, Kalign, MAVID and four versions of MANGO: MANGO8, MANGO8-r, MANGO90, MANGO90-r, on three 16S SSU rRNA benchmark data sets. Here is bali_score program from balibase (V3) to calculate SP/PS score.

prokaryotes seq aln program SP PS time mem result ClustalW-fast 0.937 0.929 00:05:24 4M aln ClustalW 0.913 0.932 01:46:20 4M aln MUSCLE-fast 0.925 0.928 00:02:25 216M aln MUSCLE 0.937 0.928 00:23:47 216M aln MAFFT-fast 0.931 0.930 00:00:42 137M aln MAFFT 0.949 0.942 01:40:06 149M aln Dialign-fast 0.924 0.934 34:11:23 409M aln Dialign 0.921 0.928 56:21:43 401M aln DIALIGN-T 0.770 0.952 05:45:19 201M aln T-Coffee - - failed - - Kalign 0.926 0.914 00:01:13 6M aln MAVID 0.903 0.966 00:01:27 14M aln MANGO8 0.929 0.942 00:02:01 49M aln MANGO8-r 0.944 0.939 00:11:00 49M aln MANGO90 0.943 0.945 00:04:59 49M aln MANGO90-r 0.944 0.943 00:09:52 49M aln mitochondrial seq aln program SP PS time mem result ClustalW-fast 0.442 0.408 00:01:03 3M aln ClustalW 0.478 0.469 00:04:02 3M aln MUSCLE-fast 0.357 0.364 00:00:30 74M aln MUSCLE 0.442 0.421 00:05:33 74M aln MAFFT-fast 0.591 0.558 00:00:33 147M aln MAFFT 0.734 0.691 00:13:49 129M aln Dialign-fast 0.538 0.777 00:17:50 34M aln Dialign 0.588 0.763 00:50:24 37M aln DIALIGN-T 0.209 0.000 00:20:02 26M aln T-Coffee 0.594 0.740 37:31:03 1000M aln Kalign 0.375 0.330 00:00:12 4M aln MAVID 0.380 0.834 00:00:28 14M aln MANGO8 0.530 0.859 00:00:04 10M aln MANGO8-r 0.595 0.739 00:09:49 89M aln MANGO90 0.590 0.878 00:00:37 10M aln MANGO90-r 0.596 0.836 00:02:35 42M aln eukaryotes seq aln program SP PS time mem result ClustalW-fast 0.874 0.844 00:05:48 5M aln ClustalW 0.844 0.866 01:06:53 5M aln MUSCLE-fast 0.588 0.675 00:02:28 186M aln MUSCLE 0.863 0.836 00:43:58 186M aln MAFFT-fast 0.887 0.874 00:01:21 192M aln MAFFT 0.905 0.880 00:57:08 147M aln Dialign-fast 0.821 0.891 07:56:44 205M aln Dialign 0.840 0.894 14:56:31 205M aln DIALIGN-T 0.761 0.936 04:18:47 112M aln T-Coffee - - failed - - Kalign 0.869 0.837 00:01:11 6M aln MAVID 0.753 0.934 00:00:56 17M aln MANGO8 0.861 0.904 00:01:15 28M aln MANGO8-r 0.896 0.880 00:38:01 72M aln MANGO90 0.887 0.911 00:05:05 29M aln MANGO90-r 0.890 0.896 00:11:01 41M aln