Open AccessSite stripping based on likelihood ratio reduction is a useful tool to evaluate the impact of non‐clock‐like behavior on viral phylogenetic reconstructions
Author(s) -
Lemey Philippe,
Salemi Marco,
Wang Bin,
Duffy Margaret,
Hall William H,
Sakseitin K,
Vandamme AnneMieke
Publication year - 2003
Publication title -
fems immunology & medical microbiology
Language(s) - English
Resource type - Journals
eISSN - 1574-695X
pISSN - 0928-8244
DOI - 10.1016/s0928-8244(03)00239-6
Subject(s) - molecular clock , coalescent theory , divergence (linguistics) , biology , phylogenetic tree , evolutionary biology , statistics , transmission (telecommunications) , stripping (fiber) , biological system , computational biology , virology , genetics , mathematics , computer science , gene , telecommunications , linguistics , philosophy , electrical engineering , engineering
The site stripping for clock detection procedure was implemented in the recently developed maximum likelihood framework for estimating evolutionary rates and divergence times in measurably evolving populations. The method was used to investigate the effect of rate variability on estimating divergence times in non‐clock‐like trees for human immunodeficiency viruses and hepatitis C viruses. We validate our approach by comparing dated coalescent nodes in molecular phylogenies with known dates of transmission. Our method was able to rapidly recover clock‐like behavior and to indicate the presence and direction of a bias when estimates of divergence times using the unstripped data were flawed.