In the fall of 2009 and in the spring of 2012, supported by the National Institute of General Medical Sciences (NIGMS) in the National Institutes of Health (NIH), we designed a course "Phylogenetic Analysis and Molecular Evolution" (PAME), the first cross-listed course across three different colleges (College of Arts and Sciences, College of Engineering, and College of Agriculture). This course was the first at the author's university. The course will be made available to graduate students and advanced undergraduate students in biology and computer science, and undergraduate student in statistics and mathematics at regional universities and colleges. The graduate students will learn how to gather sequence data, use bioinformatics tools, and analyze biological data using mathematics and statistics throughout the project. In this paper, we propose an online course on PAME facilitated with the statistical software RStudio on Amazon Web Service (AWS).