next up previous contents index
Next: environ.principal_components() clustering Up: The environ class: MODELLER Previous: environ.schedule_scale energy   Contents   Index

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.

Automatic builds 2012-08-29