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TESS 2.3: Bayesian Clustering using tessellations and Markov models for spatial population genetics

 

TESS3: Fast inference of ancestry coefficients and genome scans for selection

 

 



        

TESS implements ancestry estimation algorithms for spatial population genetic analyses. The program performs individual geographical assignment, admixture analysis, and can be used to run genome scans for selection. TESS is particularly suited to seeking genetic discontinuities in continuous populations and estimating spatially varying individual admixture proportions. TESS returns graphical displays of geographical cluster assignments or admixture proportions (depending on the model used) and textual output of the admixture Q matrix.


June 2015 -- New version TESS3: Faster and more accurate! Novelty: TESS3 runs genome scans for selection based on ancestral allele frequency differentiation statistics. Version 3: Kevin Caye - Eric Frichot (2014-2015) top

  • Download installation files, documentation and R scripts for visualizing results: All files. The program requires that Cmake is installed on your operating system
  • Documentation and examples available from the program manual.

Download the 2.3 version of TESS (Updated january 2010) top

Version 1.0: Chibiao Chen (2006) and Version 2.1+: Eric Durand (2007-2010) 

 
The reference manual, an example data set and R scripts are included in the TESS 2.3.1 package. For new users, we advice using the tessgui.exe program first. We also advice using CLUMPP and DISTRUCT for post-processing the program outputs. The important quantities to look at are the admixture/membership coefficients.


References:

  • For the admixture model: E. Durand, F. Jay, O.E. Gaggiotti, O. François (2009) Spatial inference of admixture proportions and secondary contact zones, PDF, Molecular Biology and Evolution 26:1963-1973.
  • For the graphic user interface and for comparisons with other programs: C. Chen, E. Durand, F. Forbes, O. François (2007) Bayesian clustering algorithms ascertaining spatial population structure: A new computer program and a comparison study, PDF, Molecular Ecology Notes 7:747-756.
  • A review on spatial clustering methods: O. François, E. Durand (2010) THE STATE OF THE ART - Spatially explicit Bayesian clustering models in population genetics PDF Molecular Ecology Resources, 10: 773-784.
  • For the hidden Markov Random Field model (without admixture): O. François, S. Ancelet, G. Guillot (2006) Bayesian clustering using hidden Markov random fields in spatial population genetics, PDF, Genetics, 174: 805-816.
  • Supporting Material for Chen et al. (2007) PDF, and the five and two-island data used in the simulation study five island data , d1.ZIP, d2.ZIP, d3.ZIP, d4.ZIP.
Send feedback and comments or ask assistance:
eric dot durand at berkeley dot edu
olivier dot francois at imag dot fr