You will find references to other tools in older papers, but now the situation is clear: sequence analysis is performed using R, in command line mode, and the specifically developed and well-documented package TraMineR.
Its authors are particularly gifted and devoted when its comes to documentation and training. Therefore, you do not necessarily need to learn the basics of R first: the excellent User’s Guide for TraMineR does present them in its “Appendix A”. It is also a good introduction to sequence analysis, more advanced and thorough than our own of course – a great complement.
In addition, there are many ways to get help, including a users list where the creators of the package usually answer questions very quickly. And if you work in Europe, they can probably visit your university for one of their training sessions (in English or French).
Note that most pioneering papers in sequence analysis focus of the “optimal matching” distances, as we do in our book. But there are many other things that you can do with sequences – some are easier to implement and at least as interesting. The User’s Guide will tell you all about them, esp. in “7.2 Describing and visualizing sequence data sets.” (and in chapters 7.3 and 8).