This sample thesis extends that in ../sample-thesis-0/ to incorporate color and indexing. The easiest way to compile this sample thesis on any Unix platform is to simply type make That runs the rough equivalent of these commands: pdflatex sample-thesis-1.ltx bibtex sample-thesis-1 fgrep -v fsfname sample-thesis-1.idx | makeindex -c -s sample-thesis-1.ist > sample-thesis-1.ind fgrep bioname sample-thesis-1.idx | fgrep -v '|see' | makeindex -c -s sample-thesis-1.ist > sample-thesis-1-bioname.ind fgrep fsfname sample-thesis-1.idx | fgrep -v '|see' | makeindex -c -s sample-thesis-1.ist > sample-thesis-1-fsfname.ind Repeat them FOUR (4) times to achieve consistency. If there are no indexes, then repeat just the first two commands four times. During the writing process, the fastest update is done by make pdf-pass It runs pdflatex, bibtex, and makeindex just once. If the bibliography and index are already stable, then only pdflatex needs to be run: pdflatex sample-thesis-1.ltx