Fixed a bug that was not replacing filenames with special char.

A bug fix. When ref and contig files were being copied to files/ folder, all the special character were replaced with an underscore. But when these files were being called from other functions their name still had the special character. Camilla caught the bug. it should be fixed now.

cutoff option activated

Activated the cutoff option. Now, users can pick a threshold to decide how divergent genome to include based on proportion of reference genome used for alignment

First tested version released.

This version has an installation script that installs many of the required dependencies using bioconda and cpanm.