Massimo Bernardi, MUSE,Visit the meeting web site with complete information.
Alessandro Minelli, University of Padova, and
Omar Rota-‐Stabelli, FEM.
RevBayes is a computer program that uses directed acyclic graphs
(DAG's) to specify any type of model, to hold the model and data in
memory, and to compute the likelihood of the parameters of the model.
DAG's provide a framework for the construction of modular models.
Models can easily be extended and/or parts of the model exchanged
(e.g., the substitution process and clock model) and several models
can be combined. The design of RevBayes should allow the
implementation of any extension to existing models. RevBayes is mainly
developed for Bayesian phylogenetic analyses, but it can be extended
to any inference on probabilistic models.
In this talk, I will give a brief introduction to the concept of DAG's
and how they are used to construct a model. Once the model is
specified, I will show how to simulate new observations under the
model and how to estimate its parameters. I will demonstrate this in
the RevLanguage, which is an R-like language for building DAG's for
phylogenetic problems. The RevLanguage is used interactively to
specify the model, as done with R. I will show how a full phylogenetic
model is specified, step-by-step. I will mainly focus on various
standard substitution models, relaxed clock models, and divergence
times priors. Specifically, I will show a new birth-death model with
speciation and extinction rates varying over time and use this in a
integrative analysis. In the integrative analysis I condition only on
the alignment (only the alignment is considered to be known) and
estimate the tree and divergence times simultaneously as well as the
speciation and extinction rates.
4th - 8th July 2011
Introduction
The Biennial conferences of the Systematics Association provide a forum for systematists from different disciplines to present and discuss their research. The Sixth Biennial Conference was held at Royal Botanic Garden Edinburgh in August 2007. The conference was attended by about 240 delegates from a broad international audience. The format was a mixture of open sessions and focussed thematic symposia.
MORE INFORMATION >>>
The Annual New Zealand Phylogenetics Meeting
Sunday 6th - Friday 11th February, 2011
The meeting will be held at the The Leigh Sawmill Café.
WEBSITE: http://www.math.canterbury.ac.nz/bio/events/leigh2011/
We are very excited to have Philippe Lemey presenting on Friday July
16 at noon PDT concerning
"Phylogenetic diffusion models and their applications in viral epidemiology"
Abstract:
Emerging infectious diseases continue to appear all over the world,
and importantly, they have also risen significantly over time after.
Having the potential to quickly adapt to new hosts and environments,
RNA viruses are prime candidates to emerge as global threats to human
health. Their rapid rate of evolution, however, also turns viral
genomes into valuable resources to reconstruct the spatial and
temporal processes that are shaping epidemic or endemic dynamics. In
this seminar, I will highlight recent developments in phylogenetic
diffusion models that tie together sequence evolution and geographic
history in a coherent statistical framework. Both discrete and
continuous phylogeographic models have recently been implemented in a
Bayesian statistical approach. I will position this approach among
other popular phylogeographic methods, and then focus on applications
in viral molecular epidemiology to demonstrate their use. Finally, I
will hint at future extensions that may provide entirely new
opportunities for phylogeographic hypothesis testing.
Thanks,
Erick
To attend this and other talks, learn how to connect ahead of time.
If you can't make it, don't fret-- you can always watch the recording.
The End of Lineage Sorting: Inferring species trees using *BEAST
