The following are brief descriptions of the main menu options...

Menus are listed from left to right as observed in the applications main menu bar. The keyboard shortcut, if available, is shown in square brackets following the title of the menu item. Menu items that are followed by an elipse indicate that an auxillary window will open requiring user input. If more detailed information on the option is available eslewhere a link is provided otherwise it is detailed here.

SIMMAP

About SIMMAP :
Opens a window that gives you a brief bit of information about the SIMMAP software.

Preferences... [,]:
Opens the Preferences window allowing the user to set persistent (between application launches) options. In addition, allows users to create preference files that can be turned on and off or shared with other users. For more information on setting SIMMAP preferences see the help documents here.

Hide SIMMAP [H]:
Hides SIMMAP and its windows.

Hide Others [H]:
Hides other application's windows that are currently running.

Show All :
Shows all application's windows that are currently running and open.

Quit SIMMAP [Q]:
Quits the SIMMAP application. If a simulation is running it will ask the user to confirm the request.

File

Open Data... [O]:
Opens a file browser allowing the user to select a data file. Data file names should have a *.nex or *.mcmc extension. For more on input file formats see the help pages on input files.

Open Trees... [T]:
Opens a file browser allowing the user to select a tree file. Tree file names should have a *.t, *.tre, or *.tree extension. For more on input file formats see the help pages on input files.

Open Parameters... [R]:
Opens a file browser allowing the user to select a file containing model parameters. This options is only available for molecular data and is unavailable (appears greyed out) until a data file has been opened. This file should have a *.p extension. For more on input file formats see the help pages on input files.

Open Tree Histories... :
Opens a file browser that allows the user to open a trees history file previously saved by SIMMAP. For more information on saving tree histories file and the file format see the help pages on saving raw histories.

Close Files [W]:
Closes all of the files that are currently open.

Page Setup... [P]:
Open the page setup window that allows the user to change the print setup for printing tree images displayed in the Tree View window.

Print Tree... [P]:
Prints the currently displayed tree in the Tree View window on a single page.

Data

Deselect All Cols/Rows [D]:
If a column is selected in the Data View window it is deslected leaving none of the character columns selected.

Select Character To Display... [1]:
Opens a window that allows the user to select a character from the currently opened data file to be selected in the Data View window and available for mapping.

Include/Exclude Taxa... [2]:
Allows the user to include or exclude taxa from the Data View window but does not alter the trees and therefore the analysis. To remove taxa from the analysis use the Prune Taxa From Tree(s)... option in the Trees menu. Inlcude/exclude taxa does effect saving the data matrix to a new file. In future releases of SIMMAP this option will allow users to modify both the matrix and the trees simultaneously.

Include/Exclude Characters... [3]:
Allows the user to include or exclude characters from the analysis.

Set Character Coding... [4]:
This option determines how the characters (sites) in the data set are coded.

If the data is molecular the user can select to code the data, or some region of it, as protein coding (codon). By default, when selecting to code molecular data it is enforced (turned on). This can be truned off in the configuration window or using the Enforce Molecular Coding option in the Data menu (see below).

If the data is standard (morphological, etc.) the user can select whether characters are ordered or unordered. Currently, SIMMAP treats ordered data as a linear ordering and does not support character transformation networks. For more information on character coding see here.

Enforce Molecular Coding :
This option enforces the molecular character coding set in the above menu item. When turned ON the menu shows a check mark. (If coding is on the Data View window displays characters in the coded form.) For more information on character coding see here

Set State Colors... [5]:
Sets which colors are used when displaying different character states in both the Data View window and the Tree View window. In the Data View window the color is displayed as the background while in the Tree View window colors are used to inidcate the states along branches when a character history is being shown.

Set Genetic Code... [6]:
The user can set which genetic code is used when molecular data is coded as codons (protein). Currently, SIMMAP offers 17 different genetic codes that can be enforced during an analysis of molecular data. The codes are derived from the NCBI genetic code table, version 3.8. Currently, alternate start codons are not recognized in amino acid mappings (only those listed as "ncbieaa" are used). This limitation only effects the mapping of amino acid states along the tree, showing states at the tips, and the tabulation of amino acid transitions. For more information see the help documents on genetic codes.

Data View Font Size :
This option alters the font size of the characters displayed in the Data View window.

Save Data Matrix As... [A]:
Allows the user to save the data matrix to a new file in a number of formats - Nexus, Fasta, Phylip, and plain text. A number of other options for configuring the output are available. For a more detailed description of transforming and saving data see here.

Trees

Next Tree [[ ]:
Show the next tree in the Tree View window. The character map will be cleared if the trees read into memory lacked character history iformation. If the trees read into memory contain character history information then the next tree history is displayed.

Previous Tree [] ]:
Show the previous tree in the Tree View window. The character map will be cleared if the trees read into memory lacked character history iformation. If the trees read into memory contain character history information then the previous tree history is displayed.

Go To Tree... :
Opens a window allowing the user to select the number of the tree or tree history to display in the Tree View window.

Manage Constraints... :
Constraints are definitions that define particular clades. This item opens the Manage Constraints window. For more information on constraints used in reconstructing ancestral states see here or creating constraints from the Tree View window see here.

Load Constraints From File... :
This option allows you to open the XML plist file containing constraints information. For more information on constraints see here or creating constraints from the Tree View window see here.

Save Constraints To File... :
The user can opt to save the constraints defined in the Manage Constraints window by selecting this option. The file is saved as an XML plist file. For more information on constraints see here or creating constraints from the Tree View window see here.

Assign Branch Lengths... :
Opens the Branch Length Options window allowing the user to apply, a priori, branch lengths to the trees in memory. Users can select from the following options:

1. Fixed lengths - a fixed length, v, is assigned to each branch.
   
2. Fixed tree height - a fixed height, T, is assigned to each tree in which it defines the distance from each tip node to the root. The resulting tree is ultrametric.
   
3. Random uniform - branch length values are assigned by being radomly drawn from a uniform distribution on an interval, U[x,y], determined by the user (the interval must be positive). The user can select to sort the values and assign the values by forcing small or large values to the tips.
   
4. Random exponential - branch length values are assigned by being radomly drawn from an exponential distribution defined by the parameter, λ, determined by the user (the parameter must be positive). The user can select to sort the values and assign the values by forcing small or large values to the tips.
   
5. Birth-Death (Rannala & Yang, 1996) - branch length values are assigned by sampling from the birth-death method described by Rannala and Yang (1996). The birth-death distribution is described by four parameters: the speciation rate, λ, the extinction rate, μ, the taxon sampling rate, ρ, and the tree depth or height, T. The speciation rate, taxon sampling rate, and the tree depth must be >0.

Prune Taxa From Tree(s)... :
Opens a window that allows users to select taxa that can be pruned from the tree currently in memory. This option is undoable - once taxa are excluded they can not be added back on the trees. [To add taxa back the user needs to close all files and reload files.] While taxa are pruned from the trees they are still visible in the Data View window. Exclusion of taxa from the Data View does NOT exclude the taxa from the analysis (see above). In future releases of SIMMAP this option will allow users to modify both the matrix and the trees simultaneously. For more information read more here.

Root Trees :
Selecting this option opens a window that allows users to root the trees in memory by defining a collection of outgroup species. Alternatively, the user can select to root trees from the Tree View window by selecting the Root Tree button in the window's menu bar. The root trees window offers options for including and excluding taxa from the outgroup. (Note: Only trees that are consistent with the outgroup clade are re-rooted.) Users have the option of making the outgroup paraphyletic or monophyletic to the ingroup, to include or exclude the outgroup taxa from the character analysis, and exclude trees not consistent with the outgroup from the character analysis. For additional information on this option see the help documents on rooting trees.

Deroot Trees :
This option unroots the trees making the chracters unpolarized and releasing options to exclude outgroup taxa from the analysis and excluding trees not consistent with the outgroup. Tree drawing is unchanged but has no effect on the character histories.

Outgroup Options :
Allows the user to quickly switch between inlcuding of excluding outgroup taxa from the analysis. The option currently selected is shown with a check mark.

Draw Codon as Amino Acid [A]:
Changes how codons are drawn when mapped in the Tree View window to amino acid coloring.
Draw Codon as Codon [S]:
Changes how codons are drawn when mapped in the Tree View window to codon coloring.
Draw Codon as Triplet [Z]:
Changes how codons are drawn when mapped in the Tree View window to triplet coloring. The topmost map represents the first codon position.
Tree Display Options... :
Opens a window that allows the user to modify how trees and character histories are displayed in the Tree View window. For more detailed information on modifying the tree display see here.

Turn On Tree Modifications [L]:
Activates mouse actions in the Tree View window. Using the mouse can place the cursor above a node, double-click, and open a window with options to modify tree(s) at that node. Options include rotating the left and right descendant lineages, fixing ancestral states at the node, creating a constraint, and marking the node. For more detailed information on using tree modifications see here.

Display Mouse Over Info At Nodes [J]:
Activates mouse over info at nodes of the tree being displayed in the Tree View window. When activate placing the mouse over a node displays a variety of information about the node. The examples below show the node info windows for tip and internal nodes,

Tip Node		Internal Node

Node info includes the taxon name (or node number), branch length, state (internal node displays reconstructed state or ? when a character history is not being displayed), whether the node's ancestral states have been fixed or constrained (internal nodes only), whether the node is a member of the ingroup, posterior expectation of changes since the last reset, and the number of samples used for calculating the expectation. The window will disappear after 10 seconds or when the mouse is removed from a position over the node.

Display Tree Node Indices [N]:
Each tree in memory has each internal node indexed from the root to the tips. Activating this options displays these values in the Tree View window. Values are only displayed when a character history is not being displayed.

Clear Map From Display [C]:
Clears the character map from the display and redraws the tree using the default branch color. The default branch color can be changed using the modify tree display options (for more information see here). A character map can also be cleared using the Clear Map button in the Tree View window.

Copy Tree Image as PDF to Clipboard [C]:
Copies the currently displayed tree in the Tree View window to the clipboard encoded as a pdf.

Open Tree Image in Preview :
Opens a copy of the currently displayed tree in the Tree View window in Apple's Preview application if present on the computer.

Save Tree Image to Graphics File... :
Allows the user to save the currently displayed tree in the Tree View window to a graphics file. The file can be saved as in encapsulated post script (eps) or portable document format (pdf).

Save Trees to NEXUS File... :
Saves the trees currently in memory to a new Nexus file. The file includes a translation block and branch lengths. This option does not save character histories.

Models

Set Model... [8]:
Opens the Model window allowing users to configure the subsitution model used during mapping characters. For more on models see here.

Set Morphology Priors... [9]:
Opens the Morphology Priors window allowing users to configure the morphology priors on the bias parameter (two-state characters only) and rate prior used during mapping morphological (standard) characters. For more on priors see here.

Analysis

Simulate History [M]:
Simulates a character history for the currently selected character on the currently displayed tree and displays it in the Tree View window.

Simulate Histories... [M]:
Opens the Simulate Histories window allowing the user to configure a character history analysis. For more details of simulating character histories see the tutorial or the help documents on options by window. Briefly, the Simulate Histories window contains four tabs for accessing options for customizing the simulation of character histories: Sampling, Trees, Parameters, and Miscellaneous.

Posterior Ancestral States... :
Opens the Calculate Ancestral States window for configuring or starting a reconstruction analysis. For information on ancestral state reconstruction see here.

Predictive Tests... :
Opens the Predictive Test Design window for configuring a character history hypothesis test. Currently, SIMMAP can perform predictive tests of positive selection and correlated character evolution. For more information on predictive distributions see here.

Set Random Seed... :
Allows the user to set the initial random seed value used in the stochastic portions of character mapping. By default the random seed is taken from the computer clock and calendar.

Statistics

Molecular ⇒ submenu :

Nucleotide Statistics... Opens the Nucleotide Stats window that displays a summary of all nucleotide character history statistics since the last time the data was cleared from memory. For more information on the statistics collected by SIMMAP see the help documents on molecular statistics.

Codon Statistics... Opens the Codon Stats window that displays a summary of all codon character history statistics since the last time the data was cleared from memory. For more information on the statistics collected by SIMMAP see the help documents on molecular statistics.

Nucleotide Association Statistics... Opens the Nucleotide Associations window that displays the results of a chracter correlation analysis and the predictive p-values if determined. For more information on the character correlation see the help documents on correlated characters.

Positive Selection Statistics... Opens the Syn/Non-synonymous Test window that displays the results of a test of positive selection by site or for whole gene partition. For more information on testing for positive selection see the help documents on predictive tests.

Clear Nucleotide Statistics Clears all nucleotide statistics collected from memory. This action is un-doable.

Clear Codon Statistics Clears all codon statistics collected from memory. This action is un-doable.

Morphology ⇒ submenu :

Morphology Statistics... Opens the Morphology Stats window that displays a summary of all morphological (standard) character history statistics since the last time the data was cleared from memory. For more information on the statistics collected by SIMMAP see the help documents on morphology statistics.

Morphology Association Results... Opens the Morphology Association results window displaying the output of a test for correlated character evolution. For more information see the help documents on correlated characters and predictive tests.

Clear Morphology Statistics Clears all morphology (standard) statistics collected from memory. This action is un-doable.

Set File to Save History Statistics to... :
Sets the filename and location for saving character history statistics. Also allows the user to activate saving individual and summary statistics. Both are written to the same file. See the help documents on statistics (morphology or molecular) and output files.

Set File to Save Tree Histories to... :
Sets the filename and location for saving character tree histories (raw map data). For more information on saving raw history data and the output format see the help documents here.

Set File to Save Predictive Results to... :
Sets the filename and location for saving predictive results. Predictive results are the null statistics used for testing hypotheses. This option can also be set and activated in the Miscellaneous tab of the Simulate Histories window. Set the file from the main menu does not activate the saving of predictive values. For more information on saving predictive statistics see the help documents here.

Save No. Changes To Tree File :
This option activates the saving the number of observed changes in character histories to a tree file. The changes are saved as branch lengths using the mean number of changes. To set the options and output file name and location see the option below.

Set Options & File to Save No. Changes to... :
This option opens the window shown below that allows the user to set the filename to save the number of changes on branch and how the the changes are summarized for molecular data (morphological data is simply the mean number of changes along the branch for each character.

Three options are available for molecular data:

1. Save nucleotide changes as branch lengths
   • Nulceotide changes are saved as the number of changes for each realization.
2. Save amino acid changes as branch lengths
   • Amino acid changes are saved as the number of changes for each realization.
3. Save codon changes as branch lengths
   • Codon changes are saved as the number of synonymous and non-synonymous changes for each realization. Seperate trees for each type of change are saved.

Show No. Changes Above Branches :
SIMMAP continuously saves the number of changes observed on a trees branches during single and multiple simulations. Values are stored for each tree and are displayed as the posterior expectation. This option activates the display of changes along the branch.

Clear No. Changes From Branches :
Clears the number of changes observed along a branch for each tree setting them to zero.

Tools

These options are currently unavailable and slotted for future development. For some preliminary information see here.

MrBayes

Execute Data File in MrBayes... :
Launches a MrBayes process and executes the currently loaded data file. For more information on MrBayes integration in SIMMAP see the help documents here.

Quit MrBayes... :
Quits MrBayes process started by SIMMAP.

Window

Show File Inspector [I]:
Opens the File Inspector window if closed or brings it to the front if hidden. This window displays information regarding the files currently loaded in SIMMAP.

Show Tree View :
Opens the Tree View window if closed or brings it to the front if hidden.

Show Data View :
Opens the Data View window if closed or brings it to the front if hidden.

Show Parameter View :
Opens the Parameter View window if closed or brings it to the front if hidden.

Close Window [W]:
Closes the fron most window. Some windows require this action to occur from the window and do not respond to this item.

Minituarize All :
Minituarize all open windows.

Minimize :
Minimize all open windows.

Zoom :
Zoom the foremost window to its maximum size. Not all windows can be manipulated in this way.

Bring All to Front :
Brings all hidden windows onto the screen.

Help

Help Documents [?]:
Opens the SIMMAP help documents in a built in HTML viewer.

Software License :
Opens the Software License document in the built in HTML help viewer.

How To Submit A Bug Report :
Opens the built in HTML help viewer to the page describing how to submit a bug report to the author and includes a description of Crash Reporter support built into SIMMAP.

SIMMAP Web Page :
Opens the SIMMAP web page in the default web browser.