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Analysis (Mapping)

To configure a mutational mapping analysis open the Analysis window (Figures 1,2,3) by selecting Analysis->Configure Analysis from the main menu. The window contains three tabs - General (Figure 1), Sampling (Figure 2), and Statistics (Figure 3) - covering different aspects of a mutational mapping analysis. To run an analysis use the keyboard shortcut, cmd-R, or select Analysis->Run Analysis... from the main menu.

General Tab -

                        Figure 1.


Select Mutational mapping in the Analysis Type box. The characters/sites to be analyzed can be set Characters box. The following information can be saved to a file during the analysis:

  1. Save individual statistics to file
  2. Save summary statistics to file
  3. Save mutational maps to file

For more information on saving information to files see here. For more information on mutational mapping statistics see here.

Sampling Tab -

The Sampling tab allows you to configure how SIMMAP 1.5 samples mutational histories (Figure 2). The following describes what each option does.

Number of samples: the number of mutational maps to sample for each tree and character selected for the analysis.

Number of prior draws (morphological/standard only): the number of draws (or replicate maps) from the prior distribution. This is redundant with the number of samples but is included for future development. In the future X samples will be simulated for each draw from the prior (for each tree and character). In general, it is probably best to simply set this value to 1 and increase the number of samples.

Perform predictive sampling (applies only to character correlation and non-synonymous/synonymous rate analyses; see the General tab info above): this activates posterior predictive sampling to determine p-values. For example, whether the correlation between characters is significantly greater/smaller than you would expect by chance alone.

Number of predictive samples (applies only to character correlation and non-synonymous/synonymous rate analyses; see the General tab info above): the number of predictive samples to simulate. This is a multiplier of the number of samples (and prior draws). Perform predictive sampling must be active, i.e., checked.

Save predictive maps to file (applies only to character correlation and non-synonymous/synonymous rate analyses; see the General tab info above): the posterior predictive mutational maps, generated when performing predictive sampling, are save to a Nexus tree file (w/ translate block). (See here for more details on the file written.) This allows for a custom analysis of the data, not available in SIMMAP 1.5, to be performed. Perform predictive sampling must be active, i.e., checked. A file must be defined using the Set button which allows a file name and location to be chosen.

Save predictive statistics to file (applies only to character correlation and non-synonymous/synonymous rate analyses; see the General tab info above): the posterior predictive summary statistics being tested during a predictive test are saved to a file. (See here for more details on the file written.) These are the individual values obtained from each simulated replicate. Perform predictive sampling must be active, i.e., checked. A file must be defined using the Set button which allows a file name and location to be chosen.

                        Figure 2.


Use all trees: All trees in the input control file are used. For each character and tree a replicate is performed. These values are defined by Number of samples and Number of prior draws if applicable.

Use trees numbered: A subset of trees in the input control file can be selected for an analysis. For each character and tree a replicate is performed. These values are defined by Number of samples and Number of prior draws if applicable.

Use all parameters (molecular data only and only when a model definition is contained in the input control file): All parameters in the input control file are used. For each character and tree/parameter combination a replicate is performed. This value is defined by Number of samples.

Use parameters numbered (molecular data only and only when a model definition is contained in the input control file): A subset of the parameters in the input control file can be selected for an analysis. For each character and tree/parameter combination a replicate is performed. This value is defined by Number of samples.

Link parameter order to tree order (molecular data only and only when a model definition is contained in the input control file): The parameters are linked to a particular tree and evaluated together. When this is not activated then each possible parameter and tree combination are evaluated. Warning, this can be very time consuming and for most, if not all, applications is unnecessary.

Statistics Tab -

SIMMAP 1.5 will summarize mutational maps using a variety of statistics. This tab of the analysis window allows the user to define which statistics to collect when Saving individual statistics options are selected. (Note: Summary statistics are collected automatically during an analysis and can be saved using the Summary Statistics window.)

The user can select the desired statistics to be collected for a particular type of analysis (Figure 3). A desciption of the statistics can be found here.

                        Figure 3.