Final alignment and final tree files discrepancy

[Undulapodi]

Dear authors, thank you for the very useful article!
When I investigated the tree and alignment files in /PAS_phylogenetic_trees folder, I noticed different number of sequences in tree file and alignment file.
As I understand, the sample_final-tree.txt shoul be the final tree file (represented in article), but sample_masked_msa_qcov80.fa (that should be the alignment file used for final tree building?) contains 400 less sequences in it (2365 sequences in alignment vs 2736 tips in tree). Therefore, I want to ask if is there possible to retrieve an alignment fully corresponding the tree showed in article?
Thank you!