1: Basics
2: Mutational Analysis
3: Correlation
4: Positive Selection
5: Ancestral States
6: Morphology Priors

Tutorial 1: Basics

SIMMAP 1.5's main menu is divided into a number of items (see below). Five of these are program specific. This tutorial describes loading files and the basics of accessing different aspects of the program not covered in the other tutorials. When a keyboard shortcut is available these are shown in parentheses after the description of how to accomplish the task using the mouse and buttons in the interface.

Opening an input (control) file:

To open an input file select File->Open... (Cmd-O). Once a file has been opened it can be quickly re-opened by selecting File->Open Recent and selecting the file from the submenu.

Once a file has been read the Data View window will open.

The Data View window offers a number of options which are discussed in more detail here.

Basics of the analysis window:

To open the Analysis window select Analysis->Configure Analysis... (Cmd-2).

The Analysis window is divided into three tabs which each deal with different aspects of configuring the analysis. The details of configuring specific analyses is dealt with in more detail in the other tutorials (see menu at top left) and in the Documentation. Below each of the tabs are described briefly as way of an introduction.

The General tab: Details entered here deal with the type of analysis, which characters to use in the analysis, and options for saving the results of an analysis.

The Sampling tab: Details entered here deal with the number of replicates to perform during an analysis, whether to perform a predictive analysis (applies only to Character Association and Positive Selection analyses), which trees to use, and which parameters to use, if performing a molecular analysis from parameters contained in the file.

The Satistics tab: Details entered here deal with which summary statistics to be saved when saving the results to a file during a mutational mapping analysis. These options do not affect which statistics are displayed in the user interface.

Basic miscellany, notes, and things you might want to know:

  1. Including/Excluding Characters: When characters are excluded from the Data menu these are not available for analysis. In addition, these characters will be excluded from the file if it is saved.
  2. Tree Rooting: While the program treats trees as essentially un-rooted when simulating a mutational map, the summary statistics are reported as if the tree is rooted as seen in the Tree View window. For example, a change from A->C is reported separately from C->A. If you wish to ignore the rooting these values can be combined to represent A<->C. See here for more on rooting trees.
  3. Morphology/Standard Models: Some thought and care should be given in defining the standard model (morphology priors). A couple of significant features are new in this version of SIMMAP 1.5. First, each character can now have an individually defined model, rather than applying a common model to all characters in an analysis. Second, users select an empirical prior on the state frequencies - these values are calculated from the observed frequencies in the data. The details of configuring standard character models is dealt with in detail here.
  4. Ancestral States (ASR) Analysis: Version 1.0 relied on the user defining clade constraints to perform an ASR analysis. The current version does away with this in favor of collecting results for all unique clades observed.