These are some books and special journal issues related to the molecular evolution and Phylogenetics:

http://www.amazon.com/Molecular-Evolution-Phylogenetics-Masatoshi-Nei/dp/0195135857

http://www.amazon.com/Molecular-Evolution-A-Phylogenetic-Approach/dp/0865428891

http://books.google.co.in/books/about/Molecular_Evolution_and_Phylogenetics.html?id=vtWW9bmVd1IC&redir_esc=y

http://ukcatalogue.oup.com/product/9780195135855.do

http://www.nature.com/hdy/journal/v86/n3/full/6889231a.html

http://www.math.canterbury.ac.nz/bio/pages/PhyloFiles/books.html

http://www.springer.com/life+sciences/evolutionary+%26+developmental+biology/book/978-1-4614-1742-2

I do not not have a specific text recommendation, but a general thought. If this is for a class you are teaching, do not make the textbook expensive. Pick an evolutionary biology textbook in a reasonable price range.

The one used at my school is attached:

http://www.amazon.com/Evolution-Carl-T-Bergstrom/dp/0393913414/ref=sr_1_1?s=books&ie=UTF8&qid=1388192795&sr=1-1&keywords=evolution

These are some books and special journal issues related to the molecular evolution and Phylogenetics:

http://www.amazon.com/Molecular-Evolution-Phylogenetics-Masatoshi-Nei/dp/0195135857

http://www.amazon.com/Molecular-Evolution-A-Phylogenetic-Approach/dp/0865428891

http://books.google.co.in/books/about/Molecular_Evolution_and_Phylogenetics.html?id=vtWW9bmVd1IC&redir_esc=y

http://ukcatalogue.oup.com/product/9780195135855.do

http://www.nature.com/hdy/journal/v86/n3/full/6889231a.html

http://www.math.canterbury.ac.nz/bio/pages/PhyloFiles/books.html

http://www.springer.com/life+sciences/evolutionary+%26+developmental+biology/book/978-1-4614-1742-2

Hi Brian

for me the following books are the iconic ones…check these out if you want to

http://www.amazon.com/Phylogenetics-Theory-Practice-Phylogenetic-Systematics/dp/0470905964/ref=sr_1_1?s=books&ie=UTF8&qid=1388253623&sr=1-1&keywords=molecular+phylogenetics+e+o+wiley

http://www.sinauer.com/molecular-systematics.html