TempEst 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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Maintainer


  • person_outline Andrew Rambaut <>

Publication for TEMPoral Exploration of Sequences and Trees

TempEst IN pipelines

 (3)
2018
PMCID: 5831051
PMID: 29489860
DOI: 10.1371/journal.pone.0192565

[…] better model convergence as suggested elsewhere [52–54]. recombination events in the selected sequences were not detected using recombination detection program version 3.0 [55]. finally, we used tempest version 1.5.1 [56] to explore the presence of temporal structure in the sequence data and estimated a positive correlation (correlation coefficient = 0.190) between genetic divergence […]

2015
PMCID: 4626756
PMID: 26226986
DOI: 10.1093/molbev/msv167

[…] modeling., sequences from each host were aligned by emboss needle (rice et al. 2000), and maximum-likelihood trees were built by raxml (stamatakis 2006). using these trees and the program path-o-gen (http://tree.bio.ed.ac.uk/software/pathogen/, last accessed august 8, 2015), we identified and removed any sequences that were noticeable outliers from the molecular clock. the final tree […]

2014
PMCID: 4104320
PMID: 24859245
DOI: 10.1093/molbev/msu173

[…] again be drawn from four gamma-distributed categories with mean and shape parameter optimized by maximum likelihood. the trees produced by codonphyml are unrooted. these trees were rooted using path-o-gen (http://tree.bio.ed.ac.uk/software/pathogen/, last accessed may 31, 2014) and visualized with figtree (http://tree.bio.ed.ac.uk/software/figtree/, last accessed may 31, 2014) to create […]

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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