Q: The program crashes with an "Access violation" or "RichEdit line insertion" error message.
A: There are many possible causes, mostly due to the format of the input file. Look at the screen output (Windows) or the "filename.log" file (Windows and Linux) to see if the program correctly read your input. This will often provide a clue as to the location of the problem.

Q: How do I estimate mutation age when the mutation location is known?
A: Set the "Iterate ancestral states, mutation age ..." field to 1 1 0 1 or 1 1 0 0. Because this causes the program to omit iterating over the mutation location, it must be in the correct location to start with. This can be set in the "Starting value(s) for recdist..." field.

Q: I'm trying to estimate mutation age and get a log: SING error.
A: Make sure that the true mutation location is not one of the markers, since the log of the distance between the current mutation position and each marker is used in one of the functions. (If you're iterating over the mutation location, it's OK if the mutation is actually one of the markers, since its estimated location will never be precisely the same as any of the markers).

Q: I have haplotype data and a dominant disease, but the "Genetic model" field only matters if genotypes are being used. Why?
A: The dominant version of the haplotype model is not currently implemented (Release 2.14), but will be shortly. The haplotype model currently asssumes that all haplotypes entered in the "Frequency, and loci..." field are disease bearing. Therefore this is appropriate for the case of a recessive disease, or a dominant disease where you know which haplotypes are disease-bearing and have only included them.

Q: I'm estimating mutation age, and the R statistic is near 1.000 right away. Why?
A: Currently, the R statistic for measuring convergence amongst chains is only implemented for comparing mutation locations. This will be updated in a future release.

Q: What type of acceptance proportions should I be aiming for?
A: For tree, mutation location, and allele frequency changes, the proportion acceptance should ideally be about 0.2 - 0.5. If your proportions are higher, you should try increasing the adjustment levels. If lower, decrease these values. The acceptance proportions for the ancestral and internal nodes tend to be much more difficult to get to these types of levels, and are often very low, for instance numbers less than 0.0001 are not uncommon. At the start of the run, acceptance proportions for these two parameters may stay at 0.0 for a while. This is not necessarily a problem, as it takes a certain amount of time for the tree structure to "equilibrate" properly.

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