Christensen Ole F
Bioinformatics Research Center, Aarhus University, Denmark.
Stat Appl Genet Mol Biol. 2006;5:Article18. doi: 10.2202/1544-6115.1217. Epub 2006 Jul 31.
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.
在分子进化领域，具有邻位依赖替换率的基因组替换模型最近受到了广泛关注。众所周知，核苷酸的替换并非独立于相邻核苷酸而发生，但对于这种替换过程也不可逆的现象，关注较少。在本文中，我构建了一种伪似然类型的方法，用于在具有邻位依赖替换率的不可逆替换模型中进行推断。我还构建了一种期望最大化（EM）算法来最大化伪似然。对于人类 - 小鼠比对序列数据，研究了许多不同的模型，结果表明链对称模型是合适的，而重叠双核苷酸模型与数据拟合不佳。
