The core of these lecture notes corresponds to the contents of a series of seminars held during November-December, 2003, at the Division of Biometry of the Rolf Nevanlinna Institute (RNI) (a research institute of mathematics, computer science and statistics, University of Helsinki). The seminars were organized within the “Centre of Population Genetic Analyses” at RNI. The centre is funded by a grant from the Academy of Finland.
The author thanks Professor Elja Arjas, head of the Division of Biometry, for the invitation to give these lectures and for several comments that have improved both the contents and of the presentation.
The original impetus for the studies underlying these notes was to understand certain issues in bacterial taxonomy (see e.g., Busse et.al. 1996, Gaunt et.al. 2001, Mougel et.al. 2002, Van de Peer et.al. 1993) especially when construction hidden Markov models using Hobohnm algorithm for preprocessing of sequence data.
The benefit of these lectures for their audience might be to have been exposed to many of the concepts and models that are being mentioned in the section on methods of a biological research paper like, e.g., (Gaunt et.al. 2001), and applied there, or in documents like PAML Manual (Yang 2002), MrByes Manual (Huelsenbeck and Ronquist 2001), and others.
The current version of the notes is not final; several additional sections and chapters are under construction. One obvious shortcoming of this version is that every item in the Bibliography is not necessarily referred to in the text. Some of the figures in the text have a sketchy standard.
Linköping: Linköping University Electronic Press, 2004. , 200 p.