This file contains two subdirectories: one for Gblocks-refined alignments in FASTA format and another for phylogenetic trees in Nexus format, constructed from candidate interdomain HGT events reported in Katz (2015) and updated with current NCBI data. The analysis reveals new homologs that may challenge—and potentially refute—many of the previously proposed horizontal gene transfer candidates between prokaryotes and eukaryotes in Katz (2015).