Example gallery¶
Here you will find examples on how to use COCOA-Tree, from basic examples performing default analyses in the quick start section, to more elaborate ones in the advanced usage section.
Cocoatree quick start¶
In this section, you’ll find examples to perform basic coevolution
analyses using cocoatree
Mapping original MSA, filtered MSA, PDB, and XCoRs
A minimal coevo analysis using cocoatree.perform_sca()
Advanced usage of cocoatree¶
In this section, you will find examples showing you how to use COCOA-Tree to perform coevolution analyses in detail and enabling you to modify the default parameters to better suit your datasets.
Mutual information versus SCA co-evolution metrics
Perform full SCA analysis on the S1A serine protease dataset
Visualization¶
In this section, you will find examples on how to plot COCOA-Tree’s coevolution results along with sequence metadata and phylogeny.
Plot XCoR together with (phylogenetic) tree and metadata
Plot a similarity heatmap of a XCoR along the phylogenetic tree
Datasets¶
In this section you will find descriptions of the three datasets included within COCOA-Tree and of how you can access their different objects.
