Scripts to analyze data using TreeMix. This pipeline runs TreeMix with bootstrapping, helps choose number of migration events and creates a consensus tree. It plots the maximum likelihood tree with bootstrap values, drift and residuals and calculates statistics for every migration event, such as migration support, standard error and p-values.
Hi,
I could not run the shell scripts because of some problem with parallel (Ubuntu 22.04.4 LTS) but it's not something I wanted to write. I found a small bug in maxLL function which affects the function only in rare occasions when there is only a single best tree. In the function definition (https://github.com/carolindahms/TreeMix/blob/d3cf65ebbacc410e22cd69183ad5f9c79e247f12/TreeMix_functions.R) in line 24 variable uniqueT is called that is defined in the line 34. It is enough to move this line before if starts (should be line 23).
Cheers
Maciek
Hi, I could not run the shell scripts because of some problem with parallel (Ubuntu 22.04.4 LTS) but it's not something I wanted to write. I found a small bug in
maxLL
function which affects the function only in rare occasions when there is only a single best tree. In the function definition (https://github.com/carolindahms/TreeMix/blob/d3cf65ebbacc410e22cd69183ad5f9c79e247f12/TreeMix_functions.R) in line 24 variableuniqueT
is called that is defined in the line 34. It is enough to move this line beforeif
starts (should be line 23). Cheers Maciek