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A Tour of Batch Files

Defining Substitution Models
- Simple Nucleotide Models: modeldefs.bf
- Global vesus local parameters: localglobal.bf
  - Interpretation.
  - Implementation.
More complex models
Imposing constraints on variables
- Simple Constraints: relrate.bf
Molecular Clocks
- Global clocks: molclock.bf
- Local clocks: localclocks.bf

Spencer Muse
2000-05-31

Sergei L. Kosakovsky Pond and Spencer V. Muse, 1997-2002