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
carolindahms
commented
7 months ago
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
maxLLfunction 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 variableuniqueTis called that is defined in the line 34. It is enough to move this line beforeifstarts (should be line 23). Cheers Maciek