Zobrazeno 1 - 10
of 69
pro vyhledávání: '"Woodhams, Michael"'
Autor:
Woodhams, Michael D., Sumner, Jeremy G., Liberles, David A., Charleston, Michael A., Holland, Barbara R.
Models of codon evolution are commonly used to identify positive selection. Positive selection is typically a heterogeneous process, i.e., it acts on some branches of the evolutionary tree and not others. Previous work on DNA models showed that when
Externí odkaz:
http://arxiv.org/abs/1709.05079
We present and explore a general method for deriving a Lie-Markov model from a finite semigroup. If the degree of the semigroup is $k$, the resulting model is a continuous-time Markov chain on $k$ states and, as a consequence of the product rule in t
Externí odkaz:
http://arxiv.org/abs/1709.00520
Autor:
Jordan, Gregory J., Carpenter, Raymond J., Holland, Barbara R., Beeton, Nicholas J., Woodhams, Michael D., Brodribb, Timothy J.
Publikováno v:
Proceedings: Biological Sciences, 2020 Jan . 287(1919), 1-7.
Externí odkaz:
https://www.jstor.org/stable/26917377
When the process underlying DNA substitutions varies across evolutionary history, the standard Markov models underlying standard phylogenetic methods are mathematically inconsistent. The most prominent example is the general time reversible model (GT
Externí odkaz:
http://arxiv.org/abs/1412.1525
Continuous-time Markov chains are a standard tool in phylogenetic inference. If homogeneity is assumed, the chain is formulated by specifying time-independent rates of substitutions between states in the chain. In applications, there are usually extr
Externí odkaz:
http://arxiv.org/abs/1206.1401
Autor:
Woodhams, Michael, Steane, Dorothy A., Jones, Rebecca C., Nicolle, Dean, Moulton, Vincent, Holland, Barbara R.
We investigate distances on binary (presence/absence) data in the context of a Dollo process, where a trait can only arise once on a phylogenetic tree but may be lost many times. We introduce a novel distance, the Additive Dollo Distance (ADD), which
Externí odkaz:
http://arxiv.org/abs/1203.0072
Autor:
Sumner, Jeremy, Jarvis, Peter, Fernandez-Sanchez, Jesus, Kaine, Bodie, Woodhams, Michael, Holland, Barbara
The general time reversible model (GTR) is presently the most popular model used in phylogentic studies. However, GTR has an undesirable mathematical property that is potentially of significant concern. It is the purpose of this article to give examp
Externí odkaz:
http://arxiv.org/abs/1111.0723
Publikováno v:
Systematic Biology, 2015 Jul 01. 64(4), 638-650.
Externí odkaz:
http://www.jstor.org/stable/43700040
Autor:
Woodhams, Michael, Steane, Dorothy A., Jones, Rebecca C., Nicolle, Dean, Moulton, Vincent, Holland, Barbara R.
Publikováno v:
Systematic Biology, 2013 Jan 01. 62(1), 62-77.
Externí odkaz:
http://dx.doi.org/10.1093/sysbio/sys071
Autor:
Sumner, Jeremy G., Jarvis, Peter D., Fernández-Sánchez, Jesús, Ferńandez-Sánchez, Jeśus, Kaine, Bodie T., Woodhams, Michael D., Holland, Barbara R.
Publikováno v:
Systematic Biology, 2012 Dec 01. 61(6), 1069-1074.
Externí odkaz:
https://www.jstor.org/stable/41678000