Associate professor in the Departments of
Statistics and of
Botany, at the
University of Wisconsin-Madison.
Member of the CALS
statistical consulting lab
and of the quantitative biology initiative
Maitre de Conférence at the
Paris XI, on leave (détachement).
|| 1208 Medical Science Center
341 Birge Hall (Botany)
||Botany: (608) 262 6820, Statistics: (608) 262 3901,
fax: (608) 262 0032|
|email:||ane at stat.wisc.edu|
||Department of Statistics|
University of Wisconsin-Madison
Medical Science Center
1300 University Ave.
Madison, WI 53706-1532
- Botany 940, Seminar: Phylogenetic Comparatives Methods,
New Advances in Phylogenetics Methods,
- Statistics 310,
Introduction to Mathematical Statistics II,
- Statistics 371,
Introductory Applied Statistics for the Life Sciences:
Spring 2006, Spring 2005, Fall 2004.
- Statistics 571,
Statistical Methods for Bioscience I:
2009, 2008, 2007, 2006.
- Statistics 572,
Statistical Methods for Bioscience II:
- Statistics 877,
Statistical Methods for Molecular Biology (team-taught):
- Statistics 992, Special Topics seminar,
Statistical Phylogenetics: Comparative methods.
My main research interest is the area of statistical inference
in molecular evolution for phylogenetics,
as well as in inference for trait evolution.
One of my aim is to detect what groups of genes
share the same genealogy, and to draw inference on the
distribution of genealogies across the genome. This area
involves statistical issues of model selection, hierarchical
modelling of species genealogies and gene genealogies, and
it also involves computational challenges. Indeed, molecular
data become available faster than appropriate methods of analysis.
Development of these methods is funded by the NSF
for application to the tree of
and to study
More recently, I have been interested in using phylogenetic
trees to analyze trait evolution, using the so-called 'comparative
methods'. Data collected on species (or related individuals)
do not form a random sample because they lack independence: sister
species are expected to have similar traits.
Such samples actually show a high level of dependence, and
there need to be adapted statistical methods of analysis.
I am especially interested in the effective degree of freedom
for parameters in these models. See this NSF
Bayesian species delimitation using both multiple genes and multiple traits.
includes the source code, examples, and documentation for version 2.1.2.
- Detection of whole genome duplications
from multiple gene families. Previous versions of the R package WGDgc are also available
R package for fitting phylogenetic linear regression models, using
a fast algorithm linear in the number of taxa. This algorithm replaces
matrix inversion and enables the analysis of trees with thousands of tips.
Minimum Description Length for the detection of phylogenetics breakpoints:
(as used in this GBE paper)
Bayesian Concordance Analysis.
Molecular data from multiple loci are combined to estimate
the dominant history of sampled individuals, and how much of
the genome supports each relationship.
- Test for Covarion evolution.
a modification of seq-gen. C program that simulates nucleotide
sequences under a variety of models, including the covarion models
(executable compiled under linux).
Source files: .tar.gz or
here along with a Makefile,
in case you wish to compile it on your machine
or want to adapt the code to your needs.
- alignment of DNA sequences from
an existing amino acid alignment.
Last modified: Wed Jun 4 14:28:02 CDT 2014