K-mer classification method improvement

New k-mer classification method with improved scaling

The output file names and locations have been changed for some functionalities (Sorry DJ).

kmer_classification

• kmer_distance_tree.R -> genome_kmer_distance_tree.R

• distance_inf_distinct_kmers.csv -> removed

• mash_distance.csv -> distances_for_tree/genome_mash_distance.csv

• distance_distinct_kmers.csv -> distances_for_tree/genome_distance_distinct_kmers.csv

• distance_all_kmers.csv -> distances_for_tree/genome_distance_all_kmers.csv

• core_kmers.csv -> kmer_identifiers/core_kmers.csv

• accessory_kmers.csv -> kmer_identifiers/accessory_kmers.csv

• unique_kmers.csv -> kmer_identifiers/unique_kmers.csv

• phenotype_shared_kmers.csv -> kmer_identifiers/phenotype_shared_kmers.csv

• phenotype_specific_kmers.csv -> kmer_identifiers/phenotype_specific_kmers.csv

• phenotype_exclusive_kmers.csv -> kmer_identifiers/phenotype_exclusive_kmers.csv

function_overview

• function_overview_per_group.csv -> removed
• go_overview.txt -> go_overview.csv
• pfam_overview.txt -> pfam_overview.csv
• tigrfam_overview.txt -> tigrfam_overview.csv
• interpro_overview.txt -> interpro_overview.csv
• bgc_overview.txt -> bgc_overview.csv
• phobius_overview.txt -> phobius_signalp_overview.txt
• cog_overview.txt -> cog_overview.csv

rename_phylogeny

• tree.newick_RENAMED -> tree_RENAMED.newick

msa_of_group

• informative/variable_sites.csv -> informative/variable_site_counts.csv

calculate_ANI

• ani.tree -> ANI.newick