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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 citations

 (9)
library_books

Evolution of a wild plant tobamovirus passaged through an exotic host: Fixation of mutations and increased replication

2017
Virus Evol
PMCID: 5399921
PMID: 28458912
DOI: 10.1093/ve/vex001

[…] f observed changes in the genome after passaging, no correction (i.e. determining the evolution model) was done. Calculation of the substitution rate of YTMMV (substitutions/site/year) was done using TipDate v1.2 () with the Mobyle platform set to default parameters (). YTMMV Cervantes (NC_022801) from the original host plant was used as the root of the tree. […]

library_books

Phylodynamics of the Emergence of Influenza Viruses after Cross Species Transmission

2013
PLoS One
PMCID: 3865002
PMID: 24358190
DOI: 10.1371/journal.pone.0082486

[…] f 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 to de […]

library_books

Shigella sonnei genome sequencing and phylogenetic analysis indicate recent global dissemination from Europe

2012
Nat Genet
PMCID: 3442231
PMID: 22863732
DOI: 10.1038/ng.2369

[…] enerations 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. […]

call_split

Detailed genetic analysis of hemagglutinin neuraminidase glycoprotein gene in human parainfluenza virus type 1 isolates from patients with acute respiratory infection between 2002 and 2009 in Yamagata prefecture, Japan

2011
Virol J
PMCID: 3295729
PMID: 22152158
DOI: 10.1186/1743-422X-8-533
call_split See protocol

[…] []. 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 L1) […]

call_split

Social Networks Shape the Transmission Dynamics of Hepatitis C Virus

2010
PLoS One
PMCID: 2890415
PMID: 20585651
DOI: 10.1371/journal.pone.0011170
call_split See protocol

[…] on 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 . A […]

library_books

Using Non Homogeneous Models of Nucleotide Substitution to Identify Host Shift Events: Application to the Origin of the 1918 ‘Spanish’ Influenza Pandemic Virus

2009
J Mol Evol
PMCID: 2772961
PMID: 19787384
DOI: 10.1007/s00239-009-9282-x

[…] ons in the LF calibration, instead of re-estimating the branch lengths under a clock model and a full substitution matrix implies a loss of information from the data. We used an implementation of the TipDate model (PAML; Yang ; Rambaut ) to re-estimate the ages of all internal nodes under the HKY85 model, which should address the concerns about the LF model above. The current TipDate implementatio […]

Citations

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

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