New will create an align view of sequence data. New Text will create a plain text document, which is the format of the sequence data files also.
Open will open an exising file. The default choice will open a file of sequences into a new window. You can choose "Sequence, append", or hold down the SHIFT key, to open a sequence file and append it to an existing alignment window.
Other Open options include opening a plain text file, a file of phylogeny trees in Newick format (see Phylip documentation), or a Gopher document.
Save, Save as, Save a copy in, all will save the current document to disk files. Revert will restore the open align view to the last version saved to disk.
Save selection, Saves only highlighted sequences to a new disk file. Doesn't affect save status of current full alignment document.
Print setup, print will print the current view.
Help brings up a view to page thru the help file.
Preferences will set some user preferences.