Dear,
I would like to save site-by-site likelihoods when running an analysis in the batch file mode. I followed an example called siteLikelihoods.nex which I found on the forum but this only works without rate heterogeneity. Sergei mentioned in the original mail on the forum: “This gets a little trickier if there are category (rate variation variables) involved, because the command outputs a vector of marginals for each site.”
Is it possible to get site-by-site likelihoods when rate heterogeneity is used and if so which command should be used?
Thanks,
Ellen.

Dear Sergei,
Thanks a lot for the batch file. But there is still a problem. For each analysis I use three partition. In a first analysis I used a codon model for two partitions with Global parameter estimates and REV with Rate Heterogeneity for the third partition, then your batch file is working. But when I do an analysis whit the same three partitions but with Rate Heterogeneity for all three partitions then the batch file doesn’t want to give output.
I changed your batch file a bit to get the output nicely aligned, as you can see in the attachment.
Is it because I use Rate Heterogeneity for several partitions that the batch file doesn’t work anymore? What should be added to get it working?
Thanks a lot for the help,
Ellen.