Hello, I've been running Lagrange with no problem. I started with the Python version and now I'm running the C++ one (released Aug 17, 2010) on a Mac OS 10.6. The program seems to work fine with an unconstrained data set, but whenever I try to constrain the areas of connectivity with the rate matrix the -ln goes to infinite and I don't get a reconstruction. I tried running the example from the manual (4 ranges, 2 periods) and it works fine, but the one I want to run has 5 ranges and 6 periods.

Is there any limitation on the number of possible ranges to reconstruct? I know 7 is the limit from a computational point of view.

I'm attaching my rate matrix and configuration file and will appreciate any input.

Thanks a lot

Simon

I forgot the tree file

Seems like though that your first rate matrix configuration is the problem

1 0 0 1 0 0 1 0 1 0 0 0 1 0 1 1 1 0 1 0 0 0 1 0 1

if i add a number other than zero to even one of the zeros it gets out of infinity. so there is something that is constrained there that eliminates a reasonable answer. does that make sense?

so

1 0 0 1 0.0001 0 1 0 1 0 0 0 1 0 1 1 1 0 1 0 0 0 1 0 1

will give a non-inf answer as will

1 0 0 1 0 0 1 0 1 0.0001 0 0 1 0 1 1 1 0 1 0 0 0 1 0 1

so i would make sure that those constraints are what you want (you can always of course constrain certain distributions which might make it easier as well).