Oh I see.
No, glyphIgo does not perform such an in-depth analysis, because it is not conceived to do that. Even if it can be used to subset title fonts, its main goal consists in
fast checking that a font (external to the eBook, for example a font shipped with an eReader) displays correctly the text --- irrespective to embedded fonts, font style, etc.
(The typical use case, as I wrote in the first post: you have an EPUB of the
Haft Paykar. Are all those "strange Unicode characters" going to be properly rendered by your favorite font X or are they going to appear as those nasty empty rectangles? Run glyphIgo with -e ebook.epub and -f font.ttf and you will know.)
Also, glyphIgo does not handle ligatures, if you mean whether it is able to detect them, collapse them and use the appropriate Unicode symbol. However, if a ligature is already specified as a single Unicode character, it is managed properly (as a single Unicode character).