add concat and loci folders

[roblanf]

for each dataset, we want a script which takes as input the dataset folder, and then outputs two new folders as follows:

• concat [all the files for a concatenated analysis, bar the original alignment.nex which is already in the root folder

  • alignment_partitions.nex
  • alignment_partitions.raxml

• loci

  • locus_1.nex ([i.e. locus name, then .nex])
  • locus_1_partitions.nex
  • locus_1_partitions.raxml
  • ...
  • the same three files for every locus

Then in the readme we can include command lines to do concatenated and individual locus analyses for every alignment.