Comparison of various programs over two benchmark datasets: Human versus fungal ortholog groups reported by Szklarczyk et al. (2012), and SABmark (Van Walle et al., 2005) twilight zone dataset
| . | Human remote orthologs of fungal mitochondrial proteins . | SABmark proteins . | |||||||
|---|---|---|---|---|---|---|---|---|---|
| . | Human versus S.cerevisiae (405 pairs) . | Human versus S.pombe (472 pairs) . | Twilight (10 250 pairs) . | ||||||
| Program . | %-Hits . | . | . | Compression . | %-Hits . | . | . | Compression . | %-Hits . |
| ClustalW | 71.85 | 117.4 | 2678.1 | 82.6 | 74.58 | 110.3 | 2575.0 | 77.1 | 1.7951 |
| CONTRAlign | 71.11 | 117.8 | 2679.9 | 75.7 | 72.03 | 108.8 | 2573.6 | 70.7 | 2.3512 |
| KAlign | 73.83 | 134.3 | 2639.3 | 84.9 | 74.79 | 24.8 | 2533.1 | 81.8 | 2.4878 |
| MAFFT | 70.79 | 163.9 | 2622.1 | 81.8 | 71.91 | 150.9 | 2535.7 | 76.7 | 1.8187 |
| MUSCLE | 73.83 | 136.5 | 2639.3 | 86.1 | 76.06 | 129.8 | 2539.1 | 84.9 | 2.4976 |
| ProbCons | 70.12 | 143.5 | 2639.3 | 78.9 | 71.61 | 130.4 | 2543.9 | 75.9 | 1.6683 |
| TCoffee | 69.14 | 141.8 | 2640.9 | 76.5 | 71.19 | 130.8 | 2544.4 | 71.1 | 1.6390 |
| MML () | 79.26 | 119.1 | 2666.5 | 93.7 | 80.51 | 109.5 | 2548.85 | 94.2 | 4.1399 |
| MML () | 94.57 | N/A | N/A | 125.0 | 94.49 | N/A | N/A | 117.9 | 34.9951 |
| . | Human remote orthologs of fungal mitochondrial proteins . | SABmark proteins . | |||||||
|---|---|---|---|---|---|---|---|---|---|
| . | Human versus S.cerevisiae (405 pairs) . | Human versus S.pombe (472 pairs) . | Twilight (10 250 pairs) . | ||||||
| Program . | %-Hits . | . | . | Compression . | %-Hits . | . | . | Compression . | %-Hits . |
| ClustalW | 71.85 | 117.4 | 2678.1 | 82.6 | 74.58 | 110.3 | 2575.0 | 77.1 | 1.7951 |
| CONTRAlign | 71.11 | 117.8 | 2679.9 | 75.7 | 72.03 | 108.8 | 2573.6 | 70.7 | 2.3512 |
| KAlign | 73.83 | 134.3 | 2639.3 | 84.9 | 74.79 | 24.8 | 2533.1 | 81.8 | 2.4878 |
| MAFFT | 70.79 | 163.9 | 2622.1 | 81.8 | 71.91 | 150.9 | 2535.7 | 76.7 | 1.8187 |
| MUSCLE | 73.83 | 136.5 | 2639.3 | 86.1 | 76.06 | 129.8 | 2539.1 | 84.9 | 2.4976 |
| ProbCons | 70.12 | 143.5 | 2639.3 | 78.9 | 71.61 | 130.4 | 2543.9 | 75.9 | 1.6683 |
| TCoffee | 69.14 | 141.8 | 2640.9 | 76.5 | 71.19 | 130.8 | 2544.4 | 71.1 | 1.6390 |
| MML () | 79.26 | 119.1 | 2666.5 | 93.7 | 80.51 | 109.5 | 2548.85 | 94.2 | 4.1399 |
| MML () | 94.57 | N/A | N/A | 125.0 | 94.49 | N/A | N/A | 117.9 | 34.9951 |
Note: The reported , and ‘Compression’ values are median statistics across the respective groups. These are information measures, reported in bits. (Only ‘%-Hits’ statistic is shown for SABmark dataset. For full details of other statistics, see Supplementary Section S5.) N/A = Not Applicable.
Comparison of various programs over two benchmark datasets: Human versus fungal ortholog groups reported by Szklarczyk et al. (2012), and SABmark (Van Walle et al., 2005) twilight zone dataset
| . | Human remote orthologs of fungal mitochondrial proteins . | SABmark proteins . | |||||||
|---|---|---|---|---|---|---|---|---|---|
| . | Human versus S.cerevisiae (405 pairs) . | Human versus S.pombe (472 pairs) . | Twilight (10 250 pairs) . | ||||||
| Program . | %-Hits . | . | . | Compression . | %-Hits . | . | . | Compression . | %-Hits . |
| ClustalW | 71.85 | 117.4 | 2678.1 | 82.6 | 74.58 | 110.3 | 2575.0 | 77.1 | 1.7951 |
| CONTRAlign | 71.11 | 117.8 | 2679.9 | 75.7 | 72.03 | 108.8 | 2573.6 | 70.7 | 2.3512 |
| KAlign | 73.83 | 134.3 | 2639.3 | 84.9 | 74.79 | 24.8 | 2533.1 | 81.8 | 2.4878 |
| MAFFT | 70.79 | 163.9 | 2622.1 | 81.8 | 71.91 | 150.9 | 2535.7 | 76.7 | 1.8187 |
| MUSCLE | 73.83 | 136.5 | 2639.3 | 86.1 | 76.06 | 129.8 | 2539.1 | 84.9 | 2.4976 |
| ProbCons | 70.12 | 143.5 | 2639.3 | 78.9 | 71.61 | 130.4 | 2543.9 | 75.9 | 1.6683 |
| TCoffee | 69.14 | 141.8 | 2640.9 | 76.5 | 71.19 | 130.8 | 2544.4 | 71.1 | 1.6390 |
| MML () | 79.26 | 119.1 | 2666.5 | 93.7 | 80.51 | 109.5 | 2548.85 | 94.2 | 4.1399 |
| MML () | 94.57 | N/A | N/A | 125.0 | 94.49 | N/A | N/A | 117.9 | 34.9951 |
| . | Human remote orthologs of fungal mitochondrial proteins . | SABmark proteins . | |||||||
|---|---|---|---|---|---|---|---|---|---|
| . | Human versus S.cerevisiae (405 pairs) . | Human versus S.pombe (472 pairs) . | Twilight (10 250 pairs) . | ||||||
| Program . | %-Hits . | . | . | Compression . | %-Hits . | . | . | Compression . | %-Hits . |
| ClustalW | 71.85 | 117.4 | 2678.1 | 82.6 | 74.58 | 110.3 | 2575.0 | 77.1 | 1.7951 |
| CONTRAlign | 71.11 | 117.8 | 2679.9 | 75.7 | 72.03 | 108.8 | 2573.6 | 70.7 | 2.3512 |
| KAlign | 73.83 | 134.3 | 2639.3 | 84.9 | 74.79 | 24.8 | 2533.1 | 81.8 | 2.4878 |
| MAFFT | 70.79 | 163.9 | 2622.1 | 81.8 | 71.91 | 150.9 | 2535.7 | 76.7 | 1.8187 |
| MUSCLE | 73.83 | 136.5 | 2639.3 | 86.1 | 76.06 | 129.8 | 2539.1 | 84.9 | 2.4976 |
| ProbCons | 70.12 | 143.5 | 2639.3 | 78.9 | 71.61 | 130.4 | 2543.9 | 75.9 | 1.6683 |
| TCoffee | 69.14 | 141.8 | 2640.9 | 76.5 | 71.19 | 130.8 | 2544.4 | 71.1 | 1.6390 |
| MML () | 79.26 | 119.1 | 2666.5 | 93.7 | 80.51 | 109.5 | 2548.85 | 94.2 | 4.1399 |
| MML () | 94.57 | N/A | N/A | 125.0 | 94.49 | N/A | N/A | 117.9 | 34.9951 |
Note: The reported , and ‘Compression’ values are median statistics across the respective groups. These are information measures, reported in bits. (Only ‘%-Hits’ statistic is shown for SABmark dataset. For full details of other statistics, see Supplementary Section S5.) N/A = Not Applicable.
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