Table 1 Parameters for simulating evolutionary events in gene clusters
From: Evaluation of methods for detecting conversion events in gene clusters
Event Type | Properties |
|---|---|
Duplication | Number of duplications Location of duplication Length of duplicated region Space between the original copy and the new one Orientation of the new duplicated copy |
Deletion | Number of deletions Location of deletion Length of deleted region |
Conversion | Number of conversions Length of the two paralogous sequences Space between the two paralogous sequences Relative orientation of the two paralogous sequences Location of the two paralogous sequences Location of converted region Length of converted region Direction of conversion |
Small-scale mutation | HKY substitution model Divergence rates between species |
Purifying selection | Locations of elements under purifying selection Lengths of elements Mutation rate of elements |
Other | Timing of large-scale events in each species lineage |