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Clading (Phylogenetics)

View the sequence-distance relationships between selected entries.

This tool is helpful in the evaluation of residue variations amongst closely related sequences, diversity amongst the set, and the identification of possible leads with potentially diverse developability characteristics.

The Clading tool exemplifies the core work principle to "Be Inherently Lazy"—working very hard to build an easy, reproducible, and error-eliminating method to do work. The first time I performed clading by hand to generate patent claims it took me a full day, and it would take another full day to make a minor change in region selection or groupings. Using this tool requires seconds to get the same answer.

Accessing the Tool

Select at least two antibodies in the Project View. Go to the Analysis menu and select Clading. This will open the Clading workspace in a new tab.

Clading

Using the Tool

  • Tree View: Use the phylogenetic tree to set group alignments. The Clade Distance may be set via the settings value or by dragging the Clade Distance slider.
  • Clustering: Identify families of related sequences. This may be used to evaluate functional differences between the sequences and these differences may be used to aid engineering selections and to generate IP claims around functional positions.
  • Sequence Regions for Clading: Use the Chains and Regions selection boxes to focus the residues used to build the clades.
  • Export
    • Cluster Alignments: Exports the alignments in Excel.
    • Cladogram: Exports the tree as an SVG file.
  • Engineering Mutation Designs: Click a residue to enter a mutation design used by the Engineering tab.
  • Observations: Click a residue to enter an observation for that IMGT position. These are displayed in the Observations tab and on a clicked residue.
  • Indicator Dots: Dots on a residue position indicate that there is an associated engineering design or observation at that position. Engineering mutations will appear as a small eggshell square while observations will appear as a small orange circle.