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  HyPhy Documentation: HYPHY Preferences

      HYPHY preferences dialog provides access to customizable settings of the computational program and console appearance.

     Changes to "Console Font Settings" take effect immediately, whereas any other changes will take hold when the next analysis is run.

       Some of the less obvious settings:

  • Initial Guess - HYPHY uses distances based on sequence dissimilarity and least squares fitting to come up with initial estimates for parameter values. This is the case for nucleotide data. For amino acid and codon a guess specified by Starting Value is used.
  • Deletions - See Deletions and Ambiguities.
  • Output Format - See Standard Data Formats.
  • Line Width and Gap Width - Line Width specifies how many characters per line the interleaved file will have. Gap Width determines how often a space should be inserted to separate groups of sites. These options affect how HYPHY writes sequence data to disk. See an example in Data File Formats.
  • Likelihood Format - See Standard Output Formats.
  • Number Format - Controls how many decimal places are printed by default. Most batch language files should use the 'Format' command to fine tune number display.

 
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