Do you have equations for estimating the relative (or actual) time required for heuristic searches for sequences of different length and for different numbers of sequences?
Unfortunately, the time required to complete a heuristic search cannot be estimated based on the size of a data set. There are a number of reasons why this is so; however, one important reason has to do with the quality of the data (i.e., how homoplastic the data are). Another important reason is that there is no simple expression for calculating the number of tree bisection-reconnection (TBR) or subtree pruning-regrafting (SPR) rearrangements that will be made on a given tree. That is, the shape of a starting tree will determine the total number of rearrangements that can be made using one of the aforementioned swapping techniques. The problem is further complicated by the fact that it is not known how many suboptimal trees will be found during a search before optimal trees are found, and what portion of potential rearrangements of a given tree will be performed before a better tree is found.
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