Spacing Model

In some cases, an empirical distribution of the locations of the sites within the sequences may be know. Using such a distribution will allow the algorithm to focus on the most probable locations for sites (McCue 2000). To specify a spacing distribution, enter a value for each possible position in the sequences starting at position 1 up to the maximum sequence length. Spaces, tabs and newlines are ignored. The distribution will be normalized, so it is not necessary that the values sum to 1. This distribution will apply to all sequences. The default is a uniform distribution (each position is equally likely a priori). The spacing model only applies when the recursive sampler is used.