I have been experiencing some issues with the model selection on the Datamonkey website.  It seems that some of the models are not being displayed correctly on either the model selection results or the analysis options.  For example, whenever I get model 010020 as the model chosen it displays as:
To/From      A      C      G      T
A      *      AC      1      AC
C      -      *      AC      CT
G      -      -      *      AC
T      -      -      -      *
on the model results screen.

When I go to the Analysis options screen it shows:
To/From      A      C      G      T
A      *      AC      1      AC
C      -      *      AC      AT
G      -      -      *      AC
T      -      -      -      *

If I run the analysis without making any changes it shows that model 010020 was used.  If I change it to what was shown on the model results screen it says that 010040 was used.  I am not sure what I should trust on the model results screen.  Do I trust the model number or the table?

I have noticed the same problem with several other models including 012230, 010230, 001121, and 012232.  It looks like it is always the To C From T position that is different.

Models that don't appear to have the problem are 010010 and 012342.

Hello nphage,

The model numbers should be more reliable, and 2 should always be "AT", while "CT" should always be 4.

The model matrix is printed from the model string on the model results screen, and it looks like there was an error in the logic for creating the table.

Thank you for bringing this up, and apologies for the confusion.

Hello Steven,

Thank you for the response.  I had guessed that the number was probably accurate so had been using that.  Glad it was the right choice.  I now understand what the model numbers mean as well so that will be helpful.

I just wanted to let you know that this issue has still not been fixed.  I also found that this seems to be affecting the selection of the TrN model in the Analysis Options.  If you select the TrN model (010020) it will actually display in the matrix and run the 010040 model.