CHAPTER 2 Phylogenomics and Molecular Evolution (2008)
Of Polyomaviruses, Keith A. Cr, Marcos Pérez-losada, Ryan G. Christensen, David A. Mcclellan, Raphael P. Viscidi
We provide in this chapter an overview of the basic steps to reconstruct evolutionary relationships through standard phylogeny estimation approaches as well as network approaches for sequences more...
Porter, Megan L., Cronin, Thomas W., McClellan, David A., Crandall, Keith A.
Investigations of opsin evolution outside of vertebrate systems have long been focused on insect visual pigments, whereas other groups have received little attention. Furthermore, few studies have...
Porter, Megan L., Cronin, Thomas W., McClellan, David A., Crandall, Keith A.
Investigations of opsin evolution outside of vertebrate systems have long been focused on insect visual pigments while other groups have received little attention. Furthermore, few studies have...
TreeSAAP: Selection on Amino Acid Properties using phylogenetic trees (2003)
Woolley, Steve, Johnson, Justin, Smith, Matthew J., Crandall, Keith A., McClellan, David A.
Summary: The software program TreeSAAP measures the selective influences on 31 structural and biochemical amino acid properties during cladogenesis, and performs goodness-of-fit and categorical...
McClellan, David A., McCracken, Kevin G.
We evaluated the effects of selection on the molecular evolution of the functional domains of the mammalian cytochrome b gene as it relates to physicochemical properties shown to correlate with rates...
McCracken, Kevin G., Harshman, John, McClellan, David A., Afton, Alan D.
The unwitting inclusion of convergent characters in phylogenetic estimates poses a serious problem for efforts to recover phylogeny. Convergence is not inscrutable, however, particularly when one...
Comparing Phylogenetic Codivergence between Polyomaviruses and Their Hosts
Pérez-Losada, Marcos, Christensen, Ryan G., McClellan, David A., Adams, Byron J., Viscidi, Raphael P., Demma, James C., ...
Seventy-two full genomes corresponding to nine mammalian (67 strains) and two avian (5 strains) polyomavirus species were analyzed using maximum likelihood and Bayesian methods of phylogenetic...
Comparing Phylogenetic Codivergence between Polyomaviruses and Their Hosts
Pérez-Losada, Marcos, Christensen, Ryan G., McClellan, David A., Adams, Byron J., Viscidi, Raphael P., Demma, James C., ...
Seventy-two full genomes corresponding to nine mammalian (67 strains) and two avian (5 strains) polyomavirus species were analyzed using maximum likelihood and Bayesian methods of phylogenetic...