To download an alignment for a particular family/region combination:
1) go to the Taxonomic groups section
2) search for the family using the Search box
3) click on the number below the requested genomic region to visualize the alignment
4) go to the Data button in the top left and select Export
5) click on Make file in the box to download the alignment in FASTA format

To download the complete datasets of alignments for each genomic regions use these links:

Curated alignments 27-07-2017
Complete database --> Download
Region atpF-atpH --> Download
Region psbA-trnH --> Download
Region trnL CD --> Download
Region trnL GH --> Download
Region rbcL --> Download
Region matK --> Download
Region ITS --> Download