How to merge 2 alignment files with their partitions

Question

[mila.grinblat]

Hi all

I am trying to create a tree from two alignment files. each alignment file has a partitions file with some of the partitions including more than 1 loci. I used PartitionFinder version 2.1.1 to create the partitions . Partition files look like this

charset Subset1 = 11835-11889 54810-54986 1-228;
charset Subset2 = 18497-18570 17633-18107 229-390;
charset Subset3 = 391-474;

both files are a subset of the same large alignment of the same 62 samples.

Now I need to merge them. Obviously I cannot do it manually as each partition file corresponding to its alignment file.

Is there any software that can do it? I tried using TriFusion. https://trifusion.readthedocs.io/en/latest/index.html but it didnt handle the 2 partition files (or multiple partitions in nexus format)

I have both phylip and nexus formats of the files (with a charsets list for each alignment )

Will appreciate any ideas

Thanks