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environ.principal_components() -- clustering

principal_components(matrix_file, file)
This command calculates principal components clustering for 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 projected coordinates $ p$ and $ q$ are written to file file. The output file can be used with ASGL to produce a principal components plot.

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 2011-03-29