Exporting relevant files

ParGenes outputs a lot of files, some of them irrelevant for most users (logs, binary MSAs etc.).

We provide an export script export.py to export some of the most relevant files into one single directory.

Before doing an export, please make sure that your ParGenes run successfully finished. Then run the export as follows (using one of the export options):

python pargenes/pargenes_src/export.py -i pargenes_output_directory -o export_output_directory [--best-ml-tree] [--best-ml-model] [--bootstrap-trees] [--support-values-tree] [--species-tree] [--gene-trees] [--export-all]

See python pargenes/pargenes_src/export.py -h for a description of options.

If you need to free some space on your disk, we strongly encourage you to do an export and then to remove the pargenes output directory (but make sure that the export worked before removing anything!).