EconPapers    
Economics at your fingertips  
 

Pseudo-likelihood for Non-reversible Nucleotide Substitution Models with Neighbour Dependent Rates

Christensen Ole F.
Additional contact information
Christensen Ole F.: Bioinformatics Research Center, Aarhus University, Denmark

Statistical Applications in Genetics and Molecular Biology, 2006, vol. 5, issue 1, 1-31

Abstract: 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.

Date: 2006
References: View complete reference list from CitEc
Citations: Track citations by RSS feed

Downloads: (external link)
https://doi.org/10.2202/1544-6115.1217 (text/html)
For access to full text, subscription to the journal or payment for the individual article is required.

Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.

Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text

Persistent link: https://EconPapers.repec.org/RePEc:bpj:sagmbi:v:5:y:2006:i:1:n:18

Ordering information: This journal article can be ordered from
https://www.degruyter.com/view/j/sagmb

DOI: 10.2202/1544-6115.1217

Access Statistics for this article

Statistical Applications in Genetics and Molecular Biology is currently edited by Michael P. H. Stumpf

More articles in Statistical Applications in Genetics and Molecular Biology from De Gruyter
Bibliographic data for series maintained by Peter Golla ().

 
Page updated 2021-05-07
Handle: RePEc:bpj:sagmbi:v:5:y:2006:i:1:n:18