SIMMAP Preferences
SIMMAP preferences can be set by selecting the Preferences... item under the SIMMAP [
,] menu in the main menu. Preferences are divided into five areas; Characters, Trees, Parameters, Histories, and Preferences. With exception of the last item most of the options should be self explanatory or explained elsewhere (links are provided to the appropriate pages). A brief description of each is given below.
To save the changes simply select the Save button. Changes are saved to the file selected in the Preferences tab (see below on how to change this). To cancel the changes simply select the Cancel button and the values will revert to the previous ones. The defaults that SIMMAP is distributed with can be reset by selecting the Reset SIMMAP Defaults button (this action automatically saves the results).
The default preference file (Defaults) is located in the following directory:
'/Users/yourname/Library/Preferences/SIMMAP/'.This directory contains an additional file called
PrefsPaths which contains information SIMMAP accesses to know where each of your preference files are located (they need not be located in this directory). If you delete this file when SIMMAP is launched next time it will recreate the
Defaults and
PrefsPaths files and you will need to manually add any previous custom preference files.
Characters
The following preferences can be changed and saved that effect characters and character states.
- Codon Coloring in Data/Tree View:
Two options are available: Use amino acid coloring and Use codon coloring.These options are exclusive. These options effect the coloring in both the Data View and Tree View windows. This feature determines how a cell or branch is colored.
- Genetic code:
The default genetic code can be set by selecting the desired code. For more information on the available genetic codes see here.
- State Display Colors:
The colors with which different states are displayed can be changed by selecting the desired state and then clicking the color box and selecting a new color from the color panel that is presented. If the color selected in the color panel is not reflected in the color box you can mouse click in the color panel and drag it to the box. State colors can be changed and preserved for Nucleotides, Codons, Amino Acids, and Morphological character types.
Trees
The following preferences can be changed and saved that effect how trees are displayed in the
Tree View window.
- Label Display Options:
The user can change what is displayed at the tips of the tree. The Show Labels At Tips checkbox when not selected opts for no labels to be displayed at the tips of the tree. If selected two options are available: Show taxon labels and Show states. The size of the labels and the label color can also be selected. To change the label color select the color box to right and once the color panel appears choose the desired color. If the color selected in the color panel is not reflected in the color box you can mouse click in the color panel and drag it to the box. The user can select the defualt to show Show marked nodes (marked trees) by selecting the check box. In addition, the color can be changed using the color box to the right of Mark color:.
- History Display Options:
The default way in which codon maps are displayed can be set by selecting Draw as amino acid translation, Draw as codons, or Draw as nucleotide triplets.
- Tree View Background Display Options:
The background color of the Tree View window can be set along with the buffering border between the displayed tree and the edge of the viewing area.
- Tree View Branch Display Options:
The default branch color of trees drawn in the Tree View window can be set along with the width of the branches to be displayed. The latter only effects the color of branches when a map is not being displayed or certain lineages are designated as outgroups that are excluded from the analysis.
- Codon Tip Label Display Options:
The default way in which codon states are displayed at the tips of the tree can be set by selecting Show amino acid at branch tips or Show codon at branch tips.
- Optimize Tree Display:
The speed at which trees are drawn when they are requested to be displayed during a mulitple histories simulation can be set. In general, I recommend that character histories are not displayed during a simulation of multiple histories. This substantially slows the down the program and will extend the time until completion.
Parameters
The following preferences can be changed and saved that effect how SIMMAP identifies parameter values (molecular data only) contained in parameter files. Header values are not case sensitive.
- Parameter File Header Strings:
Parameter headers are the string tokens found on the first line of the parameter file. These tokens must be an unbroken string, i.e., they can not contain white spaces as this would be interpretted as two tokens. The default values are those output by MrBayes v3.0B4 when a single partition is defined. These values can be reset by selecting the Set Values button in the lower left hand corner of the tab space.
Histories
The following preferences can be changed and saved that effect how character hsitories are simulated.
- Sampling:
The following sampling conditions can be set to be defaults: Number of realizations sampled from prior(s) (morphology), Number of realizations for each tree, each site, and Number of samples to exclude from start of files (burnin). The first two options must be positive non zero values. The total number of realizations for morphological sampling is the product of these two values and the number of trees requested. The burnin value can be set as a default but I would suggest leaving it as zero since there is no way of knowing ahead of time the amount of burnin to exclude. Also, this value can not exceed the number of samples found in the posterior estimate files (trees and parameters).
- Run Configuration:
The following run conditions can be set to be defaults: Exclude trees not consistent with outgroup, Use fixed ancestral states (if defined), and Enforce coding of molecular data (if defined). The first option determines how summary statistics are recorded with respect to defined outgroup species. The default is to include outgroup species. The second option determines whether fixed internal nodes are considered fixed or uncertain. The user can fix internal nodes and then later select to ignore these values and treat the node as unknown. (The user can also unfix nodes using the Tree Modifications option.) The last option determines whether molecular coding of the data is enforced by default. A molecular coding can be defined but not enforced.
- Morphology Priors:
The parameters describing the prior distributions used in morphological analyses can be set as defaults: Prior on Bias Parameter and Prior on Rate Parameter. A more comprehensive discussion of priors can be found here. By default the bias parameter, alpha, is set such that there is roughly equal probability of going from state 0 to state 1 and vice versa. If you wish a truly uninformative (flat) prior on the bias parameter alpha should be set to 1.0.
- Run Display Options:
The following run display options can be set to be defaults: Show history on trees during simulation and Close all windows and send to background (hide) during simulation. The first option sets SIMMAP to display character histories as they are sampled during multiple simulations (this option has no effect on generating a single map). Naturally, this will slow down the analysis considerably and in addition may need to be optimized using the Optimize Tree Display: under the Trees tab described above. The second option will close all SIMMAP windows and hide the application during simulation. Currently, there is an undiscovered bug that prevents the Simulate Histories window from being redisplayed.
Preferences
SIMMAP allows users to save different preference configurations or simply use the default preference configuration file. To select a particular preference file simply select pop up button to the right of
Select Preference Settings:. To save the currently defined set of preferences to the current file simply select the
Save button. If
Apply preference settings globally to the application windows box is checked then the settings will be applied immediately to the program operation. Unselect this if you simply wish to save the new values to the preference file but leave the program's current states unchanged. To import a SIMMAP preference file select
Import Settings and select the file in the file browser.
