Dynamic programming procedure for searching optimal models to estimate substitution rates based on the maximum-likelihood method.

ABSTRACT: The substitution rate in a gene can provide valuable information for understanding its functionality and evolution. A widely used method to estimate substitution rates is the maximum-likelihood method implemented in the CODEML program in the PAML package. A limited number of branch models, chosen based on a priori information or an interest in a particular lineage(s), are tested, whereas a large number of potential models are neglected. A complementary approach is also needed to test all or a large number of possible models to search for the globally optional model(s) of maximum likelihood. However, the computational time for this search even in a small number of sequences becomes impractically long. Thus, it is desirable to explore the most probable spaces to search for the optimal models

SUBMITTER: Zhang C 

PROVIDER: S-EPMC3093512 | biostudies-literature | 2011 May

REPOSITORIES: biostudies-literature