Sawyer's Runs Tests
This test looks for evidence of recombinational exchanges within a set of aligned sequences by determining if regions of sequence pairs have more consecutive identical polymorphic sites in common than would be expected by chance (Sawyer, 1989; Drouin et al, 1999). Pair-wise comparisons of derived sequences containing only silent polymorphic sites (condensed sequences) are made. Each pair of sequences is partitioned into fragments containing runs of identical sites. The lengths of all the fragments found between every pair-wise comparison are used to obtain two values: the sum of the squares of condensed fragments (SSCF) and the maximum condensed fragment (MCF). A gene conversion event tends to increase the values of SSCF and MCF as it results in an identical region within two sequences and may produce an unusually long fragment. Provided the mutation rate is constant across sequences, SSCF and MCF are not significantly influenced by mutational hot and cold spots.
Alternative measures of the sizes of conserved segments are obtained by performing the tests on all nucleotide sites (uncondensed sequences). For each pair-wise partition, fragment boundaries are defined by the presence of a discordant silent polymorphic site. The corresponding uncondensed fragment statistics, SSUF and MUF, are more likely to resolve large conversion events but do not control for mutational hot and cold spots.
This analysis requires both allelic profiles and the allele sequences to be loaded. Again, individual isolates may be selected or deselected from inclusion using the 'Isolate Selection' dialog reachable from the 'Options' menu. This analysis also requires that the open reading frames are identified for each locus and the program will prompt for this information. If necessary, it will take you to the 'Reading Frames' dialog where these can be auto-detected.
To run the analysis, click 'Analysis ... Tests for Recombination ... Sawyer's Runs Tests'. A dialog will then appear prompting you to select which loci to perform the tests on, the number of trials and whether you wish to analyse either condensed or uncondensed fragments, or both.
The program outputs values for SSCF, MCF, SSUF and MUF with their appropriate P values. It will also display the number and types of degenerate sites and the length and identity of the four largest fragments at each locus.
Program Output:
| Locus | SSCF | SSCF P value | MCF | MCF P value | SSUF | SSUF P value | MUF | MUF P value |
| abcZ | 93335 | 0.0000 | 54 | 1.0000 | 7270579 | 0.0000 | 433 | 1.0000 |
| adk | 6890 | 0.0342 | 15 | 0.8954 | 7852119 | 0.0958 | 444 | 0.9514 |
| aroE | 50901 | 0.0032 | 46 | 1.0000 | 15933752 | 0.6362 | 489 | 1.0000 |
Silent polymorphic sites
| Locus | Silent polymorphic sites | Twofold degenerate sites | Threefold degenerate sites | Fourfold degenerate sites | Mixed degenerate sites |
| abcZ | 54 | 19 | 4 | 13 | 18 |
| adk | 16 | 8 | 0 | 5 | 3 |
| aroE | 46 | 12 | 3 | 20 | 10 |
abcZ largest condensed fragments
| Length | Condensed Fragment | Sequences |
| 54 | 1 - 54 | abcZ2 / abcZ21 |
| 49 | 1 - 49 | abcZ1 / abcZ20 |
| 12 | 43 - 54 | abcZ1 / abcZ16 |
| 12 | 43 - 54 | abcZ1 / abcZ12 |
abcZ largest uncondensed fragments
| Length | Uncondensed Fragment | Sequences |
| 433 | 1 - 433 | abcZ2 / abcZ21 |
| 416 | 1 - 416 | abcZ1 / abcZ20 |
| 98 | 1 - 98 | abcZ1 / abcZ7 |
| 66 | 368 - 433 | abcZ1 / abcZ6 |