Feature request: multiple alignments #28
Description
Moved from there:
As far as I can tell it is not possible to estimate one tree from multiple alignments. (i.e. one tree prior, multiple alignments possibly each with its own site model). I suspect this is a common use-case (either specified this way or through a concatenated alignment with partitions). If I have this wrong then a partitioned dataset should be added to the examples vignette. If this is not currently possible it should be a priority for future development