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Phased pangenomics functionalities

Jonkheer, Eef requested to merge phased_pangenomics into develop

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
Edited by Workum, Dirk-Jan van

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