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Welcome to the ClockstaR wiki!

This is a list of future developments:

• Modify clockstar.interactive()

  • Run in topology mode and/or clock mode

  • Include model generator for model testing or choose JC for all genes

  • run RaxML for tree topologies or choose NJ

    • Run topology

      • clustering
      • gap
      • cluster matrix
      • cluster trees (medoid or consensus)

    • For every cluster of gene trees (after selecting criteria) run clock mode

      • clustering
      • gap
      • cluster matrix

• the settings should be included in a ctl file

  • data folder
  • model generator path
  • raxml path
  • ML reps
  • topology choice (medoid, consensus?, concatenate (slow))
  • run topology mode | clock mode | both
  • Any other options or suggestions?