TempEst protocols

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TempEst specifications

Information


Unique identifier OMICS_28818
Name TempEst
Alternative names TEMPoral Exploration of Sequences and Trees, Path-O-Gen
Software type Application/Script
Interface Graphical user interface
Restrictions to use None
Input data A “non-click” phylogenetic tree.
Operating system Mac OS, Windows
Computer skills Medium
Version 1.5.1
Stability Stable
Maintained Yes

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  • person_outline Andrew Rambaut <>

Publication for TEMPoral Exploration of Sequences and Trees

TempEst in pipelines

 (13)
2018
PMCID: 5790234
PMID: 29381722
DOI: 10.1371/journal.pntd.0006190

[…] there was a sufficient temporal signal in the data to proceed with molecular clock analysis, a regression of root-to-tip genetic distance against dates of the m. leprae strains was conducted using tempest []. the r2 value calculated in tempest equaled 0.6212, signifying a positive correlation between genetic divergence and time for the m. leprae strains (). therefore, the data were found […]

2018
PMCID: 5831051
PMID: 29489860
DOI: 10.1371/journal.pone.0192565

[…] assure better model convergence as suggested elsewhere [–]. recombination events in the selected sequences were not detected using recombination detection program version 3.0 []. finally, we used tempest version 1.5.1 [] to explore the presence of temporal structure in the sequence data and estimated a positive correlation (correlation coefficient = 0.190) between genetic divergence […]

2017
PMCID: 5224923
PMID: 28072390
DOI: 10.7554/eLife.20983.043

[…] there was sufficient temporal structure in the s. saprophyticus phylogeny to estimate evolutionary rates, we performed a regression of root-to-tip genetic distances against year of sampling using tempest v 1.4 (). we also attempted to estimate evolutionary rates using beast v1.8 () (rrid:scr_010228). results of both these analyses (appendix) revealed a lack of temporal structure […]

2017
PMCID: 5237338
PMID: 28086751
DOI: 10.1186/s12862-016-0845-3

[…] were generated by the neighbour joining method (with 500 bootstraps) using mega 5.1.0. sequences that might contain incorrect date information were detected in these preliminary phylogenies using path-o-gen v1.2 (http://tree.bio.ed.ac.uk/software/tempest/) and were removed from the dataset. to account for potential sampling biases in space and time, sequences were subsampled to preserve […]

2017
PMCID: 5387994
PMID: 28338960
DOI: 10.1093/gbe/evx048

[…] material, supplemental material online, together with all trees in newick format., to determine whether the sequences are suitable for time tree reconstruction by bayesian methods, we used tempest (). results are shown in supplementary material, supplemental material online. molecular clock analysis was done by using beast 2 (). xml files for beast analysis were prepared by using […]


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TempEst in publications

 (156)
PMCID: 5942634
PMID: 29768530
DOI: 10.1590/0074-02760170385

[…] in zikv genes (data available from: https://github.com/caiofreire/cub)., phylodynamic analyses - using the dates of isolation, we estimated a coarse substitution rate per site per year (µ) using path-o-gen v1.4 (http://tree.bio.ed.ac.uk/soſtware/patho- gen/) with the ml tree for non-recombinant genomic sequences (alignment available from: https://github.com/caiofreire/cub). we used beast […]

PMCID: 5923486
PMID: 29652800
DOI: 10.3390/v10040192

[…] regions of the alignment that were not a product of recombination. the largest non-recombinant region which contained the most sequences was chosen for further analysis. the dataset was assessed in tempest v1.5.1 for the suitability for divergence time estimate []. the nucleotide substitution model was selected using partitionfinder v2.1.1 []. the ml tree was estimated with the randomized […]

PMCID: 5874250
PMID: 29593225
DOI: 10.1038/s41426-018-0050-0

[…] being too large. next, raxml (version 8.2.9; http://sco.hits.org/exelixis/web/soft-ware/raxml/) was utilized to infer the parsimony tree with jtt model. the tree was then visually analyzed using tempest (version 1.5; http://tree.bio.ed.ac.uk/software/tempest/) to identify potential violations that substantially deviated from the linear regression of root-to-tip genetic distance […]

PMCID: 5862964
PMID: 29563494
DOI: 10.1038/s41467-018-03205-z

[…] this resulted in removing 1281 positions. no regions of high recombination were detected in the incx4 alignment. we applied root-to-tip correlations to test for a temporal signal in the data using tempest. there was a significantly positive slope for all three alignments (supplementary fig. –)., we applied beauti and beast v2.4.7, to estimate a timed phylogeny from an alignment of inci2 […]

PMCID: 5831051
PMID: 29489860
DOI: 10.1371/journal.pone.0192565

[…] assure better model convergence as suggested elsewhere [–]. recombination events in the selected sequences were not detected using recombination detection program version 3.0 []. finally, we used tempest version 1.5.1 [] to explore the presence of temporal structure in the sequence data and estimated a positive correlation (correlation coefficient = 0.190) between genetic divergence […]


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TempEst institution(s)
Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK; Centre for Immunity, Infection and Evolution, University of Edinburgh, Ashworth Laboratories, Edinburgh, UK; School of Public Health, University of Hong Kong, Hong Kong, China; Department of Zoology, University of Oxford, Oxford, UK
TempEst funding source(s)
Supported by EU Seventh Framework Programme (FP7/2007-2013) under Grant Agreement no. 278433-PREDEMICS and ERC Grant agreement no. 260864, the European Research Council under the European Union’s Seventh Framework Programme (FP7/2007-2013)/ERC grant agreement no. 614725-PATHPHYLODYN.

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