Phased pangenomics functionalities

This merge request will introduce and update several PanTools. See documentation.

Updated functions

1. busco_protein
2. gene_classification
3. kmer_classification
4. group_info
5. rename_phylogeny
6. create_tree_template
7. core_phylogeny
8. rename_matrix

New functionalities

1. Calculate_synteny
2. add_synteny
3. synteny_overview
4. calculate_dn_ds
5. add_repeats
6. repeat_overview
7. blast
8. genome_alignment
9. gene_retention
10. sequence_visualization