Making, opening and saving data files
Mesquite is currently designed for data files following the
NEXUS format (Maddison, D.R., D.L. Swofford, and W.P. Maddison.
1997. NEXUS: An extensible file format for systematic information.
Systematic Biology 46: 590-621) although it can import and export
files of other formats. Thus, you could create your data file
with a text editor or word processor if you followed NEXUS conventions.
However, you'll probably find it easier to use Mesquite's data
matrix editors, tree windows, and so on, to specify the information
in the data file, and let Mesquite handle the formatting issues.
Mesquite can read NEXUS files created with MacClade,
and can save files that MacClade understands.
Creating a new data file
To create a new blank data file, choose File>New
(i.e., the New menu item in the File menu). You'll be presented
with a dialog box labeled "New Set of Taxa" in which
you enter the name of the set of taxa (e.g., "Drosophila")
and the initial number of taxa. (The taxa could be species, or
sequencies, or whatever are your "terminal taxa", "Operational
Taxonomic Units", or evolutionary units.) (You can just leave
the name of the set of taxa as "Untitled" if you wish,
but that may become confusing if you ever have more than one set
of taxa in the same file.) You can later add more taxa using (List
of Taxa)List>Add Taxa or (Character
Matrix Editor)>Data>Add Taxa, or by using the
Add Taxa tool in the Character Matrix
editor.
When you make a new data file, you'll be presented with a list
of taxa. They are automatically named "taxon 1", "taxon
2", and so on. You can rename a taxon name (e.g., "D.
melanogaster", "D. willistoni", and so on) by selecting
the I-beam tool and touching it on the taxon name. There is a
submenu, (List
of Taxa)List>Alter Taxon Names>, that might offer
other ways to edit taxon names. Taxon names can also be edited
in the Character Matrix editor.
A new data file will not automatically include a matrix of character
data; you must explicitly request a new matrix (see the section
on the Character Matrix editor).
Opening an existing data file
To open an existing data file, use File>Open>File.
If Mesquite detects that the file is not a NEXUS file, it will
ask to you to choose its file format for importing.
Saving a data file
Save a data file using File>Save
File or File>Save
File As. You can also export to other formats using
File>Export.
Projects and files
Mesquite is not restricted to considering only one file at a
time, but instead can collect information from various files and
consider it together. Such a collection of files sharing information
is called a project. Implicitly when you open
a file, a project is created, one which contains only a single
file. Other files can be linked into the project using the Link
commands.
Since Mesquite can accumulate and analyze a more or less indefinitely
large collection of elements of information (several sets of taxa,
data matrices, and so on), Mesquite doesn't need to respect the
boundaries of files. That is, it could read a TAXA block from
one file on the disk, and read a data matrix for those taxa from
another file on disk, and a set of trees from another file. While
other programs can handle external treefiles or command files,
Mesquite can handle external character matrices, assumptions,
and so on.
Mesquite therefore makes a distinction between the collection
of elements of information that are currently interacting with
one another in Mesquite's calculations, and the physical files
on disk or server. The former collection, which may include information
gathered from several files, is called a project. The set of files
to which the elements of information in a project belong are said
to be linked.
Mesquite shows a list of the projects and files currently active
in the Projects and Files window:
Opening versus Including versus Linking files
In Mesquite there are three ways to read a file: Open, Include
and Link.
- Open — If a file is to be opened up independently
of any other open files, and not share information, it should
be opened using the Open submenu. A file opened in this way
is treated as belonging to a project separate from any other
files open at the time.
- Include — To read in the contents of a file and
merge them into an existing file, so that all of its information
becomes part of the existing file and is saved into that existing
file, use the Include submenu in the Open submenu.
- Link — To read in the contents of a file and add
its information to a collection of information in a project
in use, but to maintain the file separate for purposes of writing
to the disk, use the Link submenu in the File menu. A file opened
in this way will become part of the project. Because of the
interdependencies among elements of information that can exist
(list of taxa in a data file matches list of taxa in a tree
file), it is possible that editing information that belongs
to one file will also change information in a linked file.
