This is a modified version of the original University of Western Ontario (UWO) LaTeX thesis template, with Justin Veenstra the original author. I post it here as a couple colleagues (myself included) have had trouble compiling the original template.

You can use natbib to manage citations. By default, this template follows the bibliography style of The Astrophysical Journal (see also the AASTeX package).

To compile the example, run

1. pdflatex ms.tex
2. bibtex intro (if you place your references in a *.bib file)
3. bibtex appdx (if you place your references in a *.bib file)
4. pdflatex ms.tex

You can populate the template with chapters and appendices, with each as an independent TeX file.

For more info of the original template, check UWO thesis formatting page.

Hope it helps!

Quan-Zhi Ye