File menu

The file menu includes various functions for importing data into MorphoJ, for saving data and analyses to disk and opening previously saved projects, and for exporting results to other applications (e.g. to specialized packages for advanced statistics or quantitative genetic analyses).

File menu
      in MorphoJ

To create an entirely new project or to create a new dataset in the current project, MorphoJ can read raw coordinate data from files in various formats: row/column (tab- or comma-delimited text, as it can be produced with spreadsheet programs) and from the custom formats for the NTSYSpc, TPS and Morphologika programs.

MorphoJ can save all the data and analyses of a project in a special kind of XML file (a project file, by default with the extension ".morphoj") so that the project can be opened in MorphoJ at a later time. These files reflect the data structure used by MorphoJ and can contain multiple datasets and analyses. The files can be exchanged between different users of MorphoJ, even if they do not use the same computing platform (e.g. between Windows and Mac OS X). Because these files contain everything but the kitchen sink, be warned that these files tend to get rather large...

For sending project files by E-mail, it is advantageous to compress them into a ZIP file or a similar file format. This reduces the file size (the project files can get quite big!) and it also reduces the risk that the file is corrupted during the transfer.

The project files should not be edited by users. The exact arrangement of parts is critical for whether the files can be read by MorphoJ and syntax items such as commas and brackets need to be in exactly the right places. Therefore, editing may destroy the functionality of a file.

Moreover, because the MorphoJ project files are specifically designed to reflect the way MorphoJ uses the data, these files are not suitable for exchange with other programs. For analyses using other programs (e.g. specialized statistics packages), the data can be exported as tab-delimited text files, which can be used by a broad range of different software such as statistics software, spreadsheet programs etc. It is possible to export the contents of datasets (via Export Dataset) or covariance matrices (via Export Covariance Matrix) to tab-delimited text files.

A range of other information (classifiers and covariates, covariance matrices, etc.) can also be imported using the File menu. Most of this information is imported from plain text files, but phylogenies and phylogeny tree sets are imported from NEXUS files.

Finally, the File menu also contains a command to close the current project and clear all the display tabs and a command to exit from MorphoJ.