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Number of citations per year for the bioinformatics software tool TempEst
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Protocols

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 citations

 (208)
library_books

NS1 codon usage adaptation to humans in pandemic Zika virus

2018
PMCID: 5942634
PMID: 29768530
DOI: 10.1590/0074-02760170385

[…] codon 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 prog […]

call_split

Re visiting the evolution, dispersal and epidemiology of Zika virus in Asia

2018
PMCID: 5940881
PMID: 29739925
DOI: 10.1038/s41426-018-0082-5
call_split See protocol

[…] quence alignments.To estimate the evolutionary rates and time to the most recent common ancestor for the Asian lineage, BEAST v.1.8.3 was employed. Initially, the temporal structure was assessed with TempEst V.1.5.1 (http://tree.bio.ed.ac.uk/software/tempest/) plus MM-type robust regression. Subsequently, a path-stone and stepping-stone model-test was performed, determining that a strict molecular […]

call_split

Full Genome Sequencing Reveals New Southern African Territories Genotypes Bringing Us Closer to Understanding True Variability of Foot and Mouth Disease Virus in Africa

2018
Viruses
PMCID: 5923486
PMID: 29652800
DOI: 10.3390/v10040192
call_split See protocol

[…] d 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 Axeler […]

library_books

Large scale sequence analysis reveals novel human adaptive markers in PB2 segment of seasonal influenza A viruses

2018
PMCID: 5874250
PMID: 29593225
DOI: 10.1038/s41426-018-0050-0

[…] rees 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 against diverg […]

library_books

The global distribution and spread of the mobilized colistin resistance gene mcr 1

2018
Nat Commun
PMCID: 5862964
PMID: 29563494
DOI: 10.1038/s41467-018-03205-z

[…] t, 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 plasmids […]

library_books

Revisiting Francisella tularensis subsp. holarctica, Causative Agent of Tularemia in Germany With Bioinformatics: New Insights in Genome Structure, DNA Methylation and Comparative Phylogenetic Analysis

2018
Front Microbiol
PMCID: 5859110
PMID: 29593661
DOI: 10.3389/fmicb.2018.00344

[…] ximum likelihood tree was generated with Randomized Accelerated Maximum Likelihood, RaxML () in GTRGAMMA model and a bootstrap number of 500. Figures were generated using Dendroscope (). Here we used TempEst for the visualization and analysis of temporally sampled sequence data (). […]


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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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