I've been using get_homologues for E. coli pangenome analysis of approximately 20 genomes comprising different ecotypes. As input for the get homologues.pl script I have been using a directory containing my genomes in genbank format. As the manual states: "The advantage of this option is that new files can be added to the input folder in the future and previous calculations will be conserved". As my genomes of interest became available, I was able to add them to the directory without having to re-run the previous comparisons. The problem that I'm having is when I try to remove a genome from the directory. When the analysis is re-run, an error message indicates that the removed genome cannot be found and the entire analysis has to be recomputed. Is there are way to by pass this? Thanks!