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TESS specifications


Unique identifier OMICS_11319
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Version 2.1.0
Stability Stable
knitr, coda, ape, deSolve, Rcpp(≥0.11.0)
Maintained Yes


No version available



  • person_outline Sebastian Hoh

Publication for TESS

TESS citations


Examination of Clock and Adcyap1 gene variation in a neotropical migratory passerine

PLoS One
PMCID: 5764313
PMID: 29324772
DOI: 10.1371/journal.pone.0190859
call_split See protocol

[…] e size differences across Oklahoma, Louisiana, and North Carolina populations by implementing unpaired Student’s t-tests.We also implemented a spatially explicit clustering algorithm in the R program TESS3 [] and computed ancestry coefficient estimations across populations based on Clock, Adcyap1, and four putative neutral genotypes. TESS3 implements least-squares and matrix factorization [, ] pro […]


Interferential current sensory stimulation, through the neck skin, improves airway defense and oral nutrition intake in patients with dysphagia: a double blind randomized controlled trial

PMCID: 5683771
PMID: 29158670
DOI: 10.2147/CIA.S140746
call_split See protocol

[…] A portable device (Gentle Stim®; J Craft, Osaka, Japan) that can generate an IFC with a beat frequency of 50 Hz was used to carry out TESS. A prototype of the device was used in previous studies,,, without any detectable adverse effects. This device was built to stimulate the nerves inside the neck through placement of two pairs of […]


Spatial and Temporal Scales of Range Expansion in Wild Phaseolus vulgaris

Mol Biol Evol
PMCID: 5850745
PMID: 29069389
DOI: 10.1093/molbev/msx273

[…] Molecular PCA was performed using the adegenet package () implemented in the R environment. Spatial population structure was inferred with TESS3 (), an algorithm specifically developed for inferring population structure using both genetic and geographic data. The program was run with the number of populations (K) ranging from 2 to 10 and […]


Genetic structure of brown pelicans (Pelecanus occidentalis) in the northern Gulf of Mexico in the context of human management and disturbance

PLoS One
PMCID: 5627915
PMID: 28977003
DOI: 10.1371/journal.pone.0185309
call_split See protocol

[…] We ran Mantel tests with 999 permutations in GenAlEx to determine the significance of the association between the two matrices. We used the Bayesian clustering programs STRUCTURE version 2.3.4 [] and TESS version 2.3.1 [,] to infer population structure in both time periods []. We ran STRUCTURE using the admixture and correlated allele frequencies models, with a burn-in of 500,000 and data collecti […]


Testing the adaptive radiation hypothesis for the lemurs of Madagascar

R Soc Open Sci
PMCID: 5319363
PMID: 28280597
DOI: 10.1098/rsos.161014

[…] ndary (33.9 Ma) by comparing the probability of an extinction rate shift at that time period to the probability of no rate shift in a Bayesian framework (COMET algorithm, implemented in the R package TESS, []; electronic supplementary material).Lastly, I tested the relative likelihoods of multiple diversification models including those with changing speciation and/or extinction rates through time […]


Complex interplay between neutral and adaptive evolution shaped differential genomic background and disease susceptibility along the Italian peninsula

Sci Rep
PMCID: 5007512
PMID: 27582244
DOI: 10.1038/srep32513
call_split See protocol

[…] for extraction of de-identified DNA samples to be used for population genomics analyses was obtained from all participants within the framework of the study by Boattini et al.3 (protocol n. 85/2009/U/Tess approved by the Bologna S.Orsola-Malpighi University Hospital ethics committee). The present study was designed and performed in accordance with relevant guidelines and regulations and according […]

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TESS institution(s)
Department of Integrative Biology, University of California, Berkeley, CA, USA; Department of Statistics, University of California, Berkeley, CA, USA; Department of Evolution and Ecology, University of California, Davis, CA, USA; Department of Mathematics, Stockholm University, Stockholm, Sweden

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