Table 1.
uBS Performance on Simulated Data
| Simulation Scenario | Sequences/Codons | Branch 1 | Branch 2 | Branch 3 | Branch 4 | Branch 5 | FWER |
Power |
||
| rBS | uBS | rBS | uBS | |||||||
| NC1 | 4 | 0.008 | 0.006 | 0.01 | 0.007 | 0.005 | 0.043 | 0.036 | — | — |
| 8 | 0.005 | 0.005 | 0.005 | 0.015 | 0.00 | 0.044 | 0.03 | — | — | |
| NC2 | 4 | 0.014 | 0.01 | 0.016 | 0.007 | 0.07 | 0.053 | 0.053 | — | — |
| 8 | 0.005 | 0.015 | 0.01 | 0.005 | 0.000 | 0.045 | 0.035 | — | — | |
| NI | 4 | 0.006 | 0.012 | 0.009 | 0.001 | 0.005 | 0.051 | 0.033 | — | — |
| 8 | 0.03 | 0.025 | 0.01 | 0.005 | 0.005 | 0.08 | 0.07 | — | — | |
| SC | 4 | 0.005 | 0.008 | 0.004 | 0.004 | 0.101 | 0.026 | 0.02 | 0.084 | 0.101 |
| 8 | 0.015 | 0.015 | 0.000 | 0.005 | 0.38 | 0.045 | 0.035 | 0.44 | 0.38 | |
| SI1 | 4 | 0.007 | 0.007 | 0.005 | 0.007 | 0.103 | 0.033 | 0.025 | 0.082 | 0.103 |
| 8 | 0.00 | 0.015 | 0.005 | 0.015 | 0.435 | 0.06 | 0.035 | 0.495 | 0.435 | |
| SI2 | 4 | 0.116 | 0.004 | 0.008 | 0.009 | 0.07 | 0.033 | 0.021 | 0.166 | 0.176 |
| 8 | 0.53 | 0.01 | 0.01 | 0.00 | 0.195 | 0.02 | 0.02 | 0.485 | 0.630 | |
| SI3 | 4 | 0.295 | 0.484 | 0.599 | 0.667 | 0.06 | 0.017 | 0.06 | 0.353 | 0.925 |
| RS1 | 1,000 | 1 | 0.01 | 1 | 0.00 | 0.00 | 0.12 | 0.01 | 1.00 | 1.00 |
| RS1 | 2,000 | 1 | 0.00 | 1 | 0.00 | 0.08 | 0.31 | 0.08 | 1.00 | 1.00 |
| RS1 | 5,000 | 1 | 0.01 | 1 | 0.00 | 0.03 | 0.74 | 0.03 | 1.00 | 1.00 |
| RS1 | 10,000 | 1 | 0.00 | 1 | 0.01 | 0.03 | 0.97 | 0.03 | 1.00 | 1.00 |
| RS2 | 1,000 | 1 | 1 | 0.00 | 0.00 | 0.44/0.03* | 0.00 | 0.00 | 1.00 | 1.00 |
| RS2 | 2,000 | 1 | 1 | 0.00 | 0.00 | 0.83/0.02* | 0.00 | 0.00 | 1.00 | 1.00 |
| RS2 | 5,000 | 1 | 1 | 0.00 | 0.00 | 0.98/0.03* | 0.00 | 0.00 | 1.00 | 1.00 |
| RS2 | 10,000 | 1 | 1 | 0.00 | 0.00 | 1.00/0.05* | 0.00 | 0.00 | 1.00 | 1.00 |
RS1 and RS2 are described in the text and figure 1. Simulations NC1, NC2, NI, SC, SI1, SI2, and SI3 are taken from Anisimova and Yang (2007) (see table 2 therein for complete details of simulation parameters). The first three simulations (NC1, NC2, and NI) do not include any lineages under positive selection, whereas the last four include one or more lineages under selection at some sites in the alignment. Branches that experience positive selection are typeset in italic. Entries for Branch 1–Branch 5 columns show the proportion of replicates where any branch from this class was found to be under positive selection at p ≤ 0.05. FWER is the proportion of replicates where at least one branch was falsely classified as undergoing positive selection. The Power column lists the proportion of replicates for which at least one branch under positive selection was correctly classified as such. *: the second number reports the proportion of replicates where Branch 5 was reported under positive selection by rBS.