A comprehensive comparison of multiple sequence alignment programs

Thompson JD, Plewniak F, Poch O. Nucleic Acids Res. 1999, 27(13), 2682-90

Supplementary material to the above publication

Ten alignment programs were compared using test alignments from the BAliBASE benchmark alignment database. Each alignment produced by the programs was compared to the BAliBASE reference alignment. A score was calculated using the 'C' program bali_score (The source code for the program is freely available) This page gives details of the scores obtained by each of the programs in the individual tests. For a full discussion of the results, see the Nucleic Acids Research paper.

Reference 1 - Small number of colinear sequences - Short, V1

	PRRP	CLUSTALX	SAGA	DIALIGN	SB_PIMA	ML_PIMA	MULTALIGN	PILEUP8	MULTAL	HMMT
1aboA	0.560	0.687	0.529	0.359	0.312	0.312	0.703	0.521	0.526	0.181
1idy	0.606	0.705	0.342	0.018	0.145	0.062	0.566	0.080	0.080	0.138
1r69	0.837	0.481	0.550	0.406	0.681	0.366	0.325	0.562	0.225	0.100
1tvxA	0.378	0.438	0.278	0.306	0.344	0.344	0.228	0.344	0.244	0.108
1ubi	0.498	0.415	0.452	0.000	0.370	0.493	0.488	0.428	0.428	0.140
1wit	0.991	0.982	0.899	0.851	0.963	0.444	0.842	0.773	0.763	0.549
2trx	0.494	0.754	0.801	0.728	0.451	0.496	0.500	0.453	0.235	0.292

Reference 1 - Small number of colinear sequences - Medium, V1

	PRRP	CLUSTALX	SAGA	DIALIGN	SB_PIMA	ML_PIMA	MULTALIGN	PILEUP8	MULTAL	HMMT
1bbt3	0.907	0.706	0.652	0.450	0.260	0.260	0.582	0.430	0.160	0.128
1sbp	0.613	0.674	0.543	0.453	0.540	0.456	0.580	0.547	0.537	0.144
1havA	0.656	0.446	0.411	0.130	0.300	0.466	0.419	0.536	0.040	0.133
1uky	0.676	0.724	0.672	0.566	0.684	0.684	0.685	0.571	0.460	0.084
2hsdA	0.885	0.691	0.771	0.679	0.470	0.470	0.470	0.646	0.463	0.117
2pia	0.780	0.890	0.690	0.660	0.740	0.740	0.760	0.850	0.560	0.057
3grs	0.447	0.635	0.689	0.327	0.416	0.416	0.380	0.446	0.347	0.056
kinase	0.891	0.736	0.862	0.764	0.733	0.703	0.643	0.730	0.650	0.277

Reference 1 - Small number of colinear sequences - Long, V1

	PRRP	CLUSTALX	SAGA	DIALIGN	SB_PIMA	ML_PIMA	MULTALIGN	PILEUP8	MULTAL	HMMT
1ajsA	0.636	0.571	0.531	0.142	0.486	0.471	0.424	0.556	0.364	0.105
1cpt	0.862	0.827	0.780	0.829	0.792	0.792	0.835	0.865	0.777	0.156
1lvl	0.694	0.632	0.619	0.699	0.559	0.559	0.570	0.587	0.572	0.064
1pamA	0.724	0.582	0.596	0.694	0.513	0.549	0.596	0.641	0.204	0.034
1ped	0.846	0.812	0.748	0.743	0.756	0.756	0.727	0.723	0.730	0.032
2myr	0.506	0.381	0.285	0.284	0.670	0.613	0.422	0.621	0.547	0.050
4enl	0.677	0.706	0.414	0.529	0.701	0.701	0.754	0.669	0.787	0.044
gal4	0.742	0.407	0.500	0.581	0.445	0.445	0.368	0.543	0.406	0.055

Reference 1 - Small number of colinear sequences - Short, V2

	PRRP	CLUSTALX	SAGA	DIALIGN	SB_PIMA	ML_PIMA	MULTALIGN	PILEUP8	MULTAL	HMMT
1aab	1.000	1.000	0.823	1.000	1.000	1.000	1.000	1.000	1.000	0.214
1fjlA	1.000	1.000	0.993	1.000	1.000	1.000	1.000	1.000	1.000	0.436
1hfh	0.933	0.917	0.945	0.410	0.868	0.932	0.936	0.848	0.883	0.261
1hpi	0.918	0.861	0.916	0.785	0.909	0.909	0.890	0.859	0.852	0.962
1csy	0.949	1.000	0.969	0.980	0.976	0.968	0.981	0.932	0.935	0.779
1pfc	0.975	0.988	0.994	0.894	0.927	0.927	0.975	0.964	0.861	0.350
1tgxA	0.895	0.806	0.873	0.871	0.782	0.768	0.819	0.718	0.651	0.556
1ycc	0.856	0.935	0.837	0.749	0.815	0.815	0.932	0.939	0.940	0.217
3cyr	0.907	0.805	0.908	0.750	0.887	0.887	0.858	0.854	0.841	0.454
451c	0.681	0.719	0.662	0.729	0.541	0.552	0.683	0.668	0.713	0.346

Reference 1 - Small number of colinear sequences - Medium, V2

	PRRP	CLUSTALX	SAGA	DIALIGN	SB_PIMA	ML_PIMA	MULTALIGN	PILEUP8	MULTAL	HMMT
1ad2	0.943	0.984	0.917	0.960	0.934	0.934	0.960	0.960	0.975	0.341
1aym3	0.976	0.969	0.955	0.962	0.976	0.958	0.969	0.952	0.969	0.567
1gdoA	0.926	0.929	0.907	0.810	0.911	0.911	0.935	0.882	0.840	0.604
1ldg	1.000	0.963	0.989	0.966	0.996	0.996	0.989	0.958	0.956	0.326
1mrj	1.000	1.000	0.949	0.977	1.000	1.000	0.994	1.000	1.000	0.561
1pgtA	0.969	1.000	0.982	0.996	0.993	1.000	0.937	0.975	1.000	0.545
1pii	0.883	0.864	0.896	0.890	0.832	0.788	0.884	0.854	0.859	0.193
1ton	0.965	0.935	0.945	0.867	0.904	0.844	0.899	0.826	0.749	0.512
2cba	0.946	0.926	0.946	0.941	0.928	0.935	0.855	0.846	0.859	0.176

Reference 1 - Small number of colinear sequences - Long, V2

	PRRP	CLUSTALX	SAGA	DIALIGN	SB_PIMA	ML_PIMA	MULTALIGN	PILEUP8	MULTAL	HMMT
1ac5	0.940	0.992	0.911	0.926	0.941	0.941	0.942	0.898	0.896	0.236
1bgl	0.979	0.959	0.972	0.959	0.934	0.929	0.959	0.958	0.977	0.365
1dlc	0.977	0.961	0.916	0.897	0.952	0.952	0.980	0.984	0.926	0.427
1eft	0.934	0.911	0.910	0.925	0.926	0.926	0.929	0.913	0.895	0.289
1fieA	0.965	0.944	0.947	0.979	0.905	0.926	0.958	0.958	0.939	0.637
1gowA	0.749	0.898	0.814	0.902	0.872	0.872	0.878	0.921	0.927	0.396
1pkm	0.942	0.921	0.955	0.927	0.907	0.911	0.946	0.931	0.851	0.748
1sesA	0.985	0.968	0.954	0.968	0.899	0.899	0.973	0.963	0.882	0.642
2ack	0.909	0.907	0.904	0.882	0.907	0.880	0.848	0.870	0.766	0.524
arp	0.956	0.945	0.933	0.930	0.914	0.927	0.938	0.925	0.927	0.293
glg	0.982	0.941	0.972	0.959	0.978	0.968	0.954	0.977	0.943	0.689

Reference 1 - Small number of colinear sequences - Short, V3

	PRRP	CLUSTALX	SAGA	DIALIGN	SB_PIMA	ML_PIMA	MULTALIGN	PILEUP8	MULTAL	HMMT
1aho	0.990	0.971	1.000	1.000	1.000	1.000	0.913	0.938	0.938	0.789
1csp	0.943	0.993	0.993	0.980	1.000	1.000	0.987	1.000	0.625	0.776
1dox	0.887	0.919	0.879	0.859	0.868	0.868	0.799	0.812	0.480	0.806
1fkj	0.982	0.981	0.981	0.958	0.944	0.987	0.951	0.913	0.609	0.879
1fmb	0.959	0.981	0.979	0.959	0.952	0.952	0.995	0.995	0.556	0.863
1krn	1.000	1.000	0.993	1.000	0.986	0.986	0.993	1.000	1.000	0.944
1plc	0.979	0.934	0.958	0.931	0.904	0.875	0.964	0.958	0.946	0.797
2fxb	0.945	0.945	0.951	0.945	0.945	0.945	0.945	0.945	0.945	0.930
2mhr	0.980	0.985	0.952	0.951	0.975	0.908	0.962	0.965	0.961	0.803
9rnt	0.965	0.974	0.965	0.864	0.970	0.961	0.965	0.970	0.974	0.832

Reference 1 - Small number of colinear sequences - Medium, V3

	PRRP	CLUSTALX	SAGA	DIALIGN	SB_PIMA	ML_PIMA	MULTALIGN	PILEUP8	MULTAL	HMMT
1amk	0.986	0.989	0.997	0.993	0.987	0.987	0.991	0.993	0.992	0.941
1ar5A	0.971	0.994	0.971	0.920	0.994	0.963	0.990	0.980	0.980	0.903
1ezm	0.941	0.948	0.932	0.911	0.956	0.956	0.958	0.948	0.610	0.851
1led	0.969	0.946	0.923	0.516	0.987	0.930	0.940	0.933	0.882	0.761
1ppn	0.973	0.989	0.983	0.648	0.962	0.979	0.973	0.978	0.973	0.856
1pysA	0.931	0.922	0.906	0.936	0.935	0.935	0.926	0.931	0.917	0.616
1thm	0.956	0.961	0.956	0.946	0.971	0.971	0.966	0.961	0.936	0.697
1tis	0.971	0.977	0.953	0.971	0.951	0.965	0.942	0.985	0.971	0.846
1zin	0.988	0.977	0.977	0.966	0.916	0.916	0.954	0.961	0.927	0.894
5ptp	0.977	0.966	0.940	0.888	0.966	0.960	0.954	0.972	0.953	0.742

Reference 1 - Small number of colinear sequences - Long, V3

	PRRP	CLUSTALX	SAGA	DIALIGN	SB_PIMA	ML_PIMA	MULTALIGN	PILEUP8	MULTAL	HMMT
1ad3	0.972	0.968	0.967	0.963	0.962	0.962	0.979	0.970	0.971	0.738
1gpb	0.988	0.986	0.982	0.958	0.964	0.964	0.987	0.983	0.964	0.650
1gtr	0.992	0.986	0.995	0.994	0.961	0.961	0.976	0.995	0.990	0.796
1lcf	0.980	0.981	0.967	0.947	0.962	0.964	0.979	0.971	0.968	0.854
1rthA	0.961	0.977	0.960	0.958	0.962	0.952	0.966	0.982	0.956	0.856
1taq	0.963	0.963	0.931	0.889	0.961	0.934	0.944	0.942	0.880	0.691
3pmg	0.987	0.995	0.989	0.985	0.985	0.985	0.994	0.994	0.993	0.844
actin	0.979	0.965	0.965	0.968	0.968	0.980	0.975	0.969	0.962	0.788

Reference 2 - 1 orphan

	PRRP	CLUSTALX	SAGA	DIALIGN	HMMT	SB_PIMA	ML_PIMA	MULTALIGN	PILEUP8
1aboA	0.256	0.650	0.489	0.384	0.724	0.391	0.220	0.528	0.000
1idy	0.370	0.515	0.548	0.000	0.353	0.000	0.000	0.401	0.000
1csy	0.350	0.154	0.154	0.000	0.000	0.000	0.000	0.154	0.114
1r69	0.675	0.675	0.475	0.675	0.000	0.675	0.675	0.675	0.450
1tvxA	0.207	0.552	0.448	0.000	0.276	0.241	0.241	0.138	0.345
1tgxA	0.695	0.727	0.773	0.630	0.622	0.678	0.543	0.696	0.318
1ubi	0.056	0.482	0.492	0.000	0.053	0.129	0.129	0.000	0.000
1wit	0.760	0.557	0.694	0.724	0.641	0.469	0.463	0.500	0.476
2trx	0.870	0.870	0.870	0.734	0.739	0.850	0.702	0.870	0.870
1sbp	0.231	0.217	0.374	0.043	0.214	0.043	0.054	0.186	0.177
1havA	0.520	0.480	0.448	0.000	0.194	0.259	0.238	0.500	0.493
1uky	0.351	0.656	0.476	0.216	0.395	0.256	0.306	0.585	0.562
2hsdA	0.404	0.484	0.498	0.262	0.423	0.390	0.561	0.593	0.278
2pia	0.767	0.752	0.763	0.612	0.647	0.730	0.695	0.765	0.766
3grs	0.363	0.192	0.282	0.350	0.141	0.183	0.211	0.192	0.159
kinase	0.896	0.848	0.867	0.692	0.749	0.755	0.651	0.830	0.799
1ajsA	0.227	0.324	0.311	0.000	0.242	0.000	0.000	0.311	0.227
1cpt	0.821	0.660	0.776	0.425	0.388	0.184	0.277	0.777	0.688
1lvl	0.772	0.746	0.726	0.783	0.539	0.620	0.688	0.614	0.678
1pamA	0.711	0.761	0.623	0.576	0.530	0.393	0.386	0.566	0.702
1ped	0.881	0.834	0.835	0.773	0.696	0.651	0.647	0.741	0.749
2myr	0.582	0.904	0.825	0.840	0.443	0.727	0.750	0.894	0.786
4enl	0.668	0.375	0.739	0.122	0.213	0.096	0.092	0.384	0.224

Reference 3 - Sub-groups of sequences

	PRRP	CLUSTALX	SAGA	DIALIGN	HMMT	SB_PIMA	ML_PIMA	MULTALIGN	PILEUP8
1idy	0.000	0.273	0.364	0.000	0.227	0.000	0.000	0.045	0.000
1r69	0.905	0.524	0.524	0.524	0.000	0.000	0.905	0.000	0.000
1ubi	0.415	0.146	0.585	0.000	0.366	0.000	0.000	0.000	0.268
1wit	0.742	0.565	0.484	0.500	0.323	0.645	0.323	0.242	0.210
1uky	0.139	0.130	0.269	0.139	0.037	0.083	0.148	0.241	0.083
kinase	0.783	0.720	0.758	0.650	0.478	0.541	0.682	0.688	0.599
1ajsA	0.128	0.163	0.186	0.000	0.006	0.000	0.000	0.000	0.110
1 pamA	0.683	0.678	0.579	0.683	0.169	0.546	0.590	0.546	0.754
1ped	0.679	0.627	0.646	0.641	0.172	0.450	0.507	0.665	0.722
2myr	0.646	0.538	0.494	0.272	0.101	0.278	0.494	0.253	0.310
4enl	0.736	0.547	0.672	0.050	0.050	0.393	0.438	0.652	0.498

Reference 4 - N/C terminal extensions

	PRRP	CLUSTALX	SAGA	DIALIGN	SB_PIMA	ML_PIMA	MULTALIGN	PILEUP8
1dynA	0.000	0.000	0.000	0.600	0.600	0.600	0.000	0.000
1pysA	0.000	0.000	0.250	0.750	1.000	1.000	0.000	0.750
1ckaA	1.000	0.000	0.375	1.000	1.000	0.000	0.000	1.000
1csp	0.000	0.000	0.000	0.889	0.000	0.000	0.000	0.000
1lkl	1.000	1.000	0.000	1.000	1.000	1.000	0.000	1.000
1mfa	0.385	1.000	0.385	1.000	0.846	1.000	0.385	1.000
1pfc	1.000	0.969	1.000	0.719	1.000	1.000	1.000	1.000
1vln	0.000	0.879	0.606	0.545	0.636	0.576	0.636	0.848
1ycc	0.485	0.485	0.485	0.727	0.970	0.818	0.485	0.455
2abk	0.000	0.000	0.000	1.000	0.471	0.471	0.000	0.471
kinase1	0.000	0.000	0.000	1.000	1.000	1.000	0.000	1.000
kinase2	0.000	0.000	0.364	1.000	1.000	1.000	1.000	1.000

Reference 5 - internal insertions

	PRRP	CLUSTALX	SAGA	DIALIGN	SB_PIMA	ML_PIMA	MULTALIGN	PILEUP8
1pysA	0.429	0.429	0.429	0.762	0.190	0.762	0.429	0.190
1eft	0.211	0.000	0.000	0.579	0.000	0.000	0.000	0.211
1ivy	1.000	0.735	0.735	1.000	1.000	0.882	0.735	1.000
1qpg	1.000	1.000	0.521	1.000	1.000	1.000	1.000	1.000
1thm1	0.765	0.412	0.765	0.765	0.765	0.412	0.412	0.765
1thm2	0.645	0.774	0.774	1.000	0.194	0.194	0.774	0.645
2cba	0.867	0.717	0.767	1.000	0.533	0.767	0.550	0.600
S51	0.662	0.938	0.831	0.646	0.338	0.631	0.646	0.646
S52	1.000	1.000	1.000	1.000	0.515	0.515	1.000	0.515
kinase1	1.000	0.806	0.484	0.806	0.677	0.677	1.000	0.677
kinase2	0.489	1.000	0.667	0.667	0.556	0.444	0.333	0.689
kinase3	0.333	0.646	0.729	0.812	0.333	0.583	0.646	0.729