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Table 1 Executables in the STK. List of all executables contained in the STK along with a short description

From: The Supertree Tool Kit

Script Name Function
Stk_amalagamate_trees Create a single file from multiple tree files.
Stk_check_data Provides a consistency check on the current dataset.
Stk_check_overlap Ensures minimal taxonomic overlap between source trees in the dataset.
Stk_check_substitutions Checks that a substitution file will not introduce taxa into a dataset. Also checks formatting of a file.
Stk_create_matrix Create a MRP matrix file from a dataset.
Stk_data_independence Check the dataset for independence between source trees.
Stk_data_summary Prints a summary of a dataset, including taxa list and some basic statistics.
Stk_fix_treeview Converts tree files produced in TreeView [20] to standard NEXUS format.
Stk_replace_genera Converts a dataset to species-level (as far as possible).
Stk_replace_taxa Enables substitutions or removal of taxa from a dataset or file.
Stk_search_data Searches phylogenetic- and meta-data. Can also create a copy from the returned results.
Stk_tree_permutation Uses a modified NEXUS file to create all permutations of taxa positions for paraphyletic taxa.