Your list_file contains the names of all genomes used to generate the persistent genome, 1 genome name per line, without extension. 'align' subcommand will then use the files in ``Proteins`` folder, called ``<genome_name_given>.prt`` and those in ``Genes`` folder, called ``<genome_name_given>.gen`` to do the alignments. ``Proteins`` and ``Genes`` folders are in your given ``<dbdir>``. You can use a file with multiple columns (like the LSTINFO file generated by 'annotate' subcommand), but only the first column will be taken into account. If you use the file generated by annotate step, you can keep it as it is (its header will be recognized). If you create your own file, do not put any header line.
.. warning:: Genome names must not contain any space.
