Basic Usage

Required input is a text file of a list of paths to fasta files genomes_list and a path to an output directory output_dir. All the genomes must be circular and complete. If you have all your genomes in one directory, you can navigate to that directory and generate genomes_list by running

ls -d -1 $PWD/*.fasta > input.txt

Then usage is

pling cluster align input.txt output_dir