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TimeTree specifications

Information


Unique identifier OMICS_14936
Name TimeTree
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Not allowed
Version 2.0
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/TimeTree

Maintainer


  • person_outline Stephen Blair Hedges

Additional information


https://itunes.apple.com/us/app/timetree/id372842500?mt=8

Publications for TimeTree

TimeTree citations

 (150)
library_books

Trabecular architecture in the sciuromorph femoral head: allometry and functional adaptation

2018
PMCID: 5954450
PMID: 29785282
DOI: 10.1186/s40851-018-0093-z

[…] The sciuromorph phylogenetic tree used herein (Fig. ) is based on a previous study [] and complemented with species from the TimeTree database [] (Gliridae, Tamiops swinhoei, Tamiops rodolphii, Aplodontia rufa, Heliosciurus rufobrachium) using Mesquite version 3.04 []. Given the apparent correlation of the lifestyle categor […]

library_books

The Phytophthora cactorum genome provides insights into the adaptation to host defense compounds and fungicides

2018
Sci Rep
PMCID: 5916904
PMID: 29695739
DOI: 10.1038/s41598-018-24939-2

[…] phylogeny using a maximum likelihood (ML) approach. To estimate the divergence time of each species, the information about the already known divergence time data between these species from http://www.timetree.org/ were collected. The topology of the ML tree was fed to MCMCTREE in paml version 4.4 for constructing a divergence time tree and calculated the divergence time. Based on the calculated ph […]

library_books

Genomics analysis of Aphanomyces spp. identifies a new class of oomycete effector associated with host adaptation

2018
BMC Biol
PMCID: 5907361
PMID: 29669603
DOI: 10.1186/s12915-018-0508-5

[…] To assess the phylogenetic position and divergence times of A. astaci, A. euteiches, and A. stellatus within oomycetes, we followed the methodology of Matari and Blair [], who produced a robust timetree of oomycetes. We used the amino acid alignments of 40 genes that were assembled for 17 oomycetes and one outgroup species (Tetrahymena thermophila), to which we added the sequences of the thr […]

library_books

Tracing the evolution of the heterotrimeric G protein α subunit in Metazoa

2018
BMC Evol Biol
PMCID: 5896119
PMID: 29642851
DOI: 10.1186/s12862-018-1147-8

[…] NOTUNG v.2.8.1.7 [] was utilized to reconcile the known species tree as extracted from timetree [] with the bootstrapped maximum likelihood gene tree generated by RAxML including all Holozoa species investigated. The root was chosen randomly from a set of roots proposed by NOTUNG which […]

library_books

Allometry and Ecology of the Bilaterian Gut Microbiome

2018
MBio
PMCID: 5874926
PMID: 29588401
DOI: 10.1128/mBio.00319-18

[…] omic levels queried (PERMANOVA P < 10−6 for phylum, class, order, family, genus, and species). In another analytic approach, evolutionary times of divergence among all host species were obtained from TimeTree (), and the resulting host evolutionary distance matrix was compared to the unweighted UniFrac matrix using the Mantel test. The level of overlay of the two matrices was found to be significa […]

library_books

Phylogenetic analysis of the CDGSH iron sulfur binding domain reveals its ancient origin

2018
Sci Rep
PMCID: 5859297
PMID: 29556009
DOI: 10.1038/s41598-018-23305-6

[…] to change among the branches of the tree and had the BLOSUM62 substitution model with γ correction for among-site rate variations. The time calibration points for each organism were obtained from the TimeTree website www.timetree.org.All BEAST Monte Carlo Markov Chain (MCMC) simulations were run for at least 50 million steps, with subsampling at every 1,000 steps. The trees generated by BEAST were […]

Citations

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TimeTree institution(s)
Department of Biology, Pennsylvania State University, University Park, PA, USA; Center for Evolutionary Functional Genomics, The Biodesign Institute and the School of Life Sciences, Arizona State University, Tempe, AZ, USA; Center for Evolutionary Medicine and Informatics, Biodesign Institute, Arizona State University, Tempe, AZ, USA; School of Life Sciences, Arizona State University, Tempe, AZ, USA
TimeTree funding source(s)
This work was supported by Research grants from the NASA Astrobiology Institute, US National Science Foundation, Science Foundation of Arizona, the US National Institutes of Health.

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