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

Create a single file from multiple tree files.

Provides a consistency check on the current dataset.

Ensures minimal taxonomic overlap between source trees in the dataset.

Checks that a substitution file will not introduce taxa into a dataset. Also checks formatting of a file.

Create a MRP matrix file from a dataset.

Check the dataset for independence between source trees.

Prints a summary of a dataset, including taxa list and some basic statistics.

Converts tree files produced in TreeView [20] to standard NEXUS format.

Converts a dataset to species-level (as far as possible).

Enables substitutions or removal of taxa from a dataset or file.

Searches phylogenetic- and meta-data. Can also create a copy from the returned results.

Uses a modified NEXUS file to create all permutations of taxa positions for paraphyletic taxa.