Index

A

add_heatmap_to_tree() (in module cocoatree.visualization)

add_sector_sequences_to_tree() (in module cocoatree.visualization)

C

cocoatree module cocoatree.datasets module cocoatree.deconvolution module cocoatree.io module cocoatree.msa module cocoatree.statistics module

cocoatree.visualization module compute_all_frequencies() (in module cocoatree.statistics) compute_apc() (in module cocoatree.statistics.pairwise) compute_conservation() (in module cocoatree.statistics.position) compute_entropy() (in module cocoatree.statistics.position) compute_entropy_correction() (in module cocoatree.statistics.pairwise) compute_mutual_information_matrix() (in module cocoatree.statistics.pairwise) compute_sca_matrix() (in module cocoatree.statistics.pairwise) compute_seq_identity() (in module cocoatree.msa) compute_seq_weights() (in module cocoatree.msa)

E

export_fasta() (in module cocoatree.io) export_sector_for_pymol() (in module cocoatree.io)

extract_independent_components() (in module cocoatree.deconvolution) extract_principal_components() (in module cocoatree.deconvolution) extract_sectors() (in module cocoatree.deconvolution)

F

filter_ref_seq() (in module cocoatree.msa)

filter_seq_id() (in module cocoatree.msa) filter_sequences() (in module cocoatree.msa)

L

load_MSA() (in module cocoatree.io) load_pdb() (in module cocoatree.io)

load_rhomboid_proteases() (in module cocoatree.datasets) load_S1A_serine_proteases() (in module cocoatree.datasets) load_tree_ete3() (in module cocoatree.io)

M

map_msa_positions() (in module cocoatree.msa) map_to_pdb() (in module cocoatree.msa) module cocoatree cocoatree.datasets cocoatree.deconvolution cocoatree.io cocoatree.msa cocoatree.statistics cocoatree.visualization

P

perform_sca() (in module cocoatree)

S

substract_first_principal_component() (in module cocoatree.deconvolution)

U

update_tree_ete3_and_return_style() (in module cocoatree.visualization)