Most of the editing can be done in the Character Matrix Editor, but some changes can be made in other windows. Below are instructions as to how to edit a character matrix. Because MacClade and Mesquite share the NEXUS file format, for most data files you will be able to edit matrices in either program to use in the other. While the Mesquite editor can handle continuous data and has special utilities, for instance to compare matrices, MacClade's editor has many features currently lacking in Mesquite's, especially concerning viewing and alignment of molecular sequence data. This is a spreadsheet editor, similar in style to MacClade's. ![]() Once you have a character matrix, you may edit it using Mesquite's Character Matrix Editor, available at the top of the Characters menu. You can also use this drop-down menu to delete a matrix. ![]() To rename a matrix from the Projects and Files window, touch on the "Character Matrix" box:Ī drop-down menu will appear with the option to rename the matrix. To delete matrices, select the rows corresponding to the matrices to be deleted, and select List>Delete Selected Character Matrices. In the List of Character Matrices window (available in the Characters menu), you can rename a matrix by editing its name directly. ![]() There are two places you can rename and delete character matrices: in the List of Character Matrices window, and in the Projects and Files window. Other choices available under Characters>Make New Matrix From> allow you to make and store matrices resulting from simulations of character evolution, randomizations of existing matrices, or other sources. If you want to create a matrix from the contents of the clipboard, select Characters>Make New Matrix From>Clipboard. For instance, if you want to make a duplicate of an existing character matrix, select Characters>Make New Matrix From>Stored Matrices. It is also possible to create character matrices that are already filled with character states. Normally, you will create an empty matrix if you are about to start entering observations about organisms. You will also need to choose the sort of data the matrix will contain (standard categorical, DNA (or RNA) sequence data, continuous, or protein sequence data). In the dialog box that appears, name the character matrix and specify the number of characters. Most simply, you can create a blank (empty) matrix by choosing Characters>New Empty Matrix. There are several ways to create a character matrix to be stored in the file. ![]() Indeed, most of Mesquite's calculations can use, instead of observed characters stored in the file, characters or matrices that are temporarily created using simulations or randomizations specifically for the purpose of the calculation. Typically the characters in these matrices stored in the file represent observations from actual organisms, but they might also be the stored results of a simulations or other hypothetical manipulation. Each matrix may have only a single type of character, but a data file may contain more than one matrix. A separate matrix may store continous characters describing measurements taken from the organisms, while a third matrix may store DNA sequence data, in which each aligned site is treated as a character (Mesquite does not currently handle fully unaligned data). Thus, one matrix may store a series of categorical characters to describe phenotypic features. Special versions of categorical characters exist for DNA, RNA and protein sequence data.Ĭharacters can exist within matrices that are stored in a data file. Mesquite supports characters whose states are categorical (discrete and not necessarily ordered) or continuous. Characters and their character states are means by which to describe the features of organisms.
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