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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