James' book chapter entitled "Evolutionary bioinformatics with a scientific computing environment" has been accepted for publication in Bioinformatics—Experimental Biology Systems, Ning-Sun Yang (Ed.), ISBN 978-953-307-280-7, by InTech. This chapter introduces the application of an emerging programming language—Matlab, in evolutionary bioinformatics. Many examples are given for preliminary and advanced analyses in molecular evolution and population genetics, with special emphasis on Matlab-based solutions. The examples relating to molecular evolution are focused on the mathematical modeling of sequence evolution; the examples relating to population genetics are focused on summary statistics and neutrality tests.