API Reference¶

`cocoatree`: Overall functions¶

Functions¶

perform_sca(sequences_id, sequences[, ...])

Perform statistical coupling analysis (SCA)

`cocoatree.io`: Functions to import and export files¶

Functions¶

`io.load_MSA`(file_path[, format, clean, verbose])	Read in a multiple sequence alignment (MSA)
`io.load_tree_ete3`(file_path)	From the loading of a Newick tree, generate a ete3.Tree object
`io.export_fasta`(sequences, sequences_id, outpath)	Export intermediate files in fasta format
`io.load_pdb`(path2pdb, pdb_id, chain)	Read in a PDB file.
`io.export_sector_for_pymol`(mapping, ...)	Export sector information for mapping on 3D structure in PyMOL.

`cocoatree.datasets`: Utilities to load popular datasets.¶

Functions¶

`datasets.load_S1A_serine_proteases`([paper])	Load the S1A serine protease dataset
`datasets.load_rhomboid_proteases`()	Load the rhomboid protease dataset

`cocoatree.msa`: Manipulating multiple sequence alignment and sequences¶

Functions¶

`msa.filter_sequences`(sequences, sequences_id)	Filter sequences
`msa.filter_seq_id`(sequences, sequences_id, ...)	Filter sequences based on list
`msa.filter_ref_seq`(sequences, sequences_id)	Filter the alignment based on identity with a reference sequence
`msa.map_to_pdb`(pdb_seq, pdb_pos, sequences, ...)	Mapping of the unfiltered MSA positions on a PDB structure.
`msa.compute_seq_identity`(sequences)	Computes the identity between sequences in a MSA (as Hamming's pairwise distance)
`msa.compute_seq_weights`(sequences[, ...])	Compute sequence weights
`msa.map_msa_positions`(n_loaded_pos, ...)	Maps positions between the original and the filtered MSA

`cocoatree.statistics`: Computation of position-specific and pairwise statistics¶

Functions¶

`statistics.compute_all_frequencies`(sequences)	Compute frequencies on sequences
`statistics.pairwise.compute_sca_matrix`(sequences)	Compute the SCA coevolution matrix
`statistics.pairwise.compute_mutual_information_matrix`(...)	Compute the mutual information matrix
`statistics.pairwise.compute_apc`(MIij)	Computes the average product correction (APC) as described in Dunn et al. (2008).
`statistics.pairwise.compute_entropy_correction`(...)	Computes the entropy correction according to Vorberg et al. (2018).
`statistics.position.compute_entropy`(aa_freq)	Computes Shannon's entropy for each position in the alignment
`statistics.position.compute_conservation`(...)	Compute the conservation of amino acid at each position.

`cocoatree.deconvolution`: Co-evolution matrix deconvolution¶

Functions¶

`deconvolution.extract_independent_components`(...)	Extract independent components from a coevolution matrix
`deconvolution.extract_principal_components`(...)	Perform principal component decomposition of a coevolution matrix
`deconvolution.extract_sectors`(...)	Extract residue positions of sectors
`deconvolution.substract_first_principal_component`(...)	Remove global correlations

`cocoatree.visualization`: Visualization with ete3¶

Module to visualize phylogenetic trees along with sectors

Functions¶

visualization.update_tree_ete3_and_return_style(...)

Update ete3 tree with sector info and attributes and return tree_style for further visualization.