Quick Examples

Some tool functions of phyclust are demonstrated in the following, and click titles to show some of phyclust features. More examples and details can be found in the phyclust vignette.

  1. Demo -- An example for quick start.

  2. File I/O -- Input and output sequence data.

  3. Trees -- Simulation studies and tree topologies by ms().

  4. ms+seqgen -- Simulation sequences according a tree.

  5. ms+seqgen+phyclust -- Bootstrap to assess the number of clusters.

  6. .EMC -- Examples of .EMControl().

  7. phyclust+paml.baseml -- Combinations of phyloclustering and maximum likelihood tree.