An example of a PHYLIP menu
(from the program DNAML)

Nucleic acid sequence Maximum Likelihood method, version 3.68
Settings for this run:
  U                 Search for best tree?  Yes
  T        Transition/transversion ratio:  2.0000
  F       Use empirical base frequencies?  Yes
  C                One category of sites?  Yes
  R           Rate variation among sites?  constant rate
  W                       Sites weighted?  No
  S        Speedier but rougher analysis?  Yes
  G                Global rearrangements?  No
  J   Randomize input order of sequences?  No. Use input order
  O                        Outgroup root?  No, use as outgroup species  1
  M           Analyze multiple data sets?  No
  I          Input sequences interleaved?  Yes
  0   Terminal type (IBM PC, ANSI, none)?  ANSI
  1    Print out the data at start of run  No
  2  Print indications of progress of run  Yes
  3                        Print out tree  Yes
  4       Write out trees onto tree file?  Yes
  5   Reconstruct hypothetical sequences?  No
  Y to accept these or type the letter for one to change

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