Environ.dendrogram() — clustering

dendrogram(matrix_file, cluster_cut)

This command calculates a clustering tree from the input matrix of pairwise distances. This matrix must be in the PHYLIP format and can be produced by the Alignment.id_table(), Alignment.compare_sequences(), or Alignment.compare_structures() commands. The weighted pair-group average clustering method (as described at Model.transfer_xyz()) is used.

The tree is written to the log file.

This command is useful for deciding about which known 3D structures are to be used as templates for comparative modeling.

Example: See Alignment.id_table() command.