TipDate statistics

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TipDate specifications

Information


Unique identifier OMICS_12357
Name TipDate
Interface Web user interface
Restrictions to use None
Input data TipDate requires a sequence alignment together with a description of the quartets and dates to be used.
Computer skills Basic
Version 1.2
Stability Stable
Maintained Yes

Documentation


Maintainer


  • person_outline Andrew Rambaut <>

Publication for TipDate

TipDate in publications

 (7)
PMCID: 3865002
PMID: 24358190
DOI: 10.1371/journal.pone.0082486

[…] the ten 'canonical' gene of each subtype was chosen according to the akaike information criterion in jmodeltest (table s5 in ). the strict molecular clock was tested with paml ver. 4.4b under the tipdate model using the trees estimated under a relaxed molecular clock implemented in beast ver. 1.6.1 ., divergence times were estimated by assuming an uncorrelated lognormal prior distribution […]

PMCID: 3442231
PMID: 22863732
DOI: 10.1038/ng.2369

[…] each) with identical substitution (gtr+γ), clock (relaxed), and demographic (bayesian skyline) models, but with randomized tip dates (). this randomization procedure produces a null set of tipdate and sequence correlations that may be analysed to produce null substitution rate distributions, which can then be compared with empirical rate estimates., the geographic region of isolation […]

PMCID: 3295729
PMID: 22152158
DOI: 10.1186/1743-422X-8-533

[…] []. to estimate the rate of molecular evolution (and hence a time scale) for a phylogeny consisting of date tips, phylogenetic analyses by ml based on the sr and srdt models were performed using the tipdate webserver http://mobyle.pasteur.fr/cgi-bin/portal.py?#forms::tipdate[]. the likelihood of the sr and srdt models (with likelihood l0) were compared to that of the dr model (with likelihood […]

PMCID: 2890415
PMID: 20585651
DOI: 10.1371/journal.pone.0011170

[…] r = ρµ, where µ is the nucleotide substitution rate (subs/site/year) and the composite parameter ρ (r/µ) estimated from the ml phylogeny, with branch lengths adjusted for date of sampling with the tipdate program . parameter d is an estimator of the generation time distribution (w(t)), which is a function that describes the distribution of times between infections in a chain of transmission . […]

PMCID: 2639529
PMID: 19146663
DOI: 10.1186/1742-4690-6-4

[…] of positive selection, a ml method was applied by using codeml implemented in the paml package and the substitution rate at individual codon position was also estimated for each patient using the tipdate model as implemented in beast . the codeml program fits various models of codon evolution to sequence data related by a phylogenetic tree, which allow to test for varying selection pressures […]


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TipDate institution(s)
Department of Zoology, University of Oxford, Oxford, UK

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