Electronic Resource
Berkeley, Calif.
:
Berkeley Electronic Press (now: De Gruyter)
Statistical applications in genetics and molecular biology
5.2006, 1, art18
ISSN:
1544-6115
Source:
Berkeley Electronic Press Academic Journals
Topics:
Biology
Notes:
In the field of molecular evolution genome substitution models with neighbour dependent substitution rates have recently received much attention. It is well-known that substitution of nucleotides does not occur independently of neighbouring nucleotides, but there has been less focus on the phenomenon that this substitution process is also not time-reversible. In this paper I construct a pseudo-likelihood type method for inference in non-reversible substitution models with neighbour dependent substitution rates. I also construct an EM-algorithm for maximising the pseudo-likelihood. For human-mouse aligned sequence data a number of different models are investigated, where I show that strand-symmetric models are appropriate, and that overlapping di-nucleotide models do not fit the data well.
Type of Medium:
Electronic Resource
URL:
http://www.bepress.com/sagmb/vol5/iss1/art18
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