21 papers · ranked by Valyu relevance
Fabia U. Battistuzzi, Qiqing Tao, Lance Jones, Koichiro Tamura + 1 more
The RelTime method estimates divergence times when evolutionary rates vary among lineages. It has been shown to perform well in the analysis of empirical and computer simulated datasets. In addition, theoretical analyses show that RelTime relaxes the strict molecular clock throughout a molecular phylogeny. However 11…
Koichiro Tamura, Qiqing Tao, Sudhir Kumar
RelTime estimates divergence times by relaxing the assumption of a strict molecular clock in a phylogeny. It showed excellent performance in estimating divergence times for both simulated and empirical molecular sequence datasets in which evolutionary rates varied extensively throughout the tree. RelTime is…
Jesus Lozano-Fernandez, Mario dos Reis, Philip C.J. Donoghue, Davide Pisani
'Davide Pisani'] Title: Abstract Establishing an accurate timescale for the history of life is crucial to understand evolutionary processes. For this purpose, relaxed molecular clock models implemented in a Bayesian MCMC framework are generally used. However, these methods are time consuming. RelTime, a non-Bayesian…
Sudhir Kumar, Koichiro Tamura
Molecular dating of species divergences has become an important means to add a temporal dimension to the Tree of Life. Increasingly larger datasets encompassing greater taxonomic diversity are becoming available to generate molecular timetrees by using sophisticated methods that model rate variation among lineages.…
Jose Barba-Montoya, Sudip Sharma, Sudhir Kumar
A common practice in molecular systematics is to infer phylogeny and then scale it to time by using a relaxed clock method and calibrations. This sequential analysis practice ignores the effect of phylogenetic uncertainty on divergence time estimates and their confidence/credibility intervals. An alternative is to…
Qiqing Tao, Koichiro Tamura, Beatriz Mello, Sudhir Kumar
Confidence intervals (CIs) depict the statistical uncertainty surrounding evolutionary divergence time estimates. They capture variance contributed by the finite number of sequences and sites used in the alignment, deviations of evolutionary rates from a strict molecular clock in a phylogeny, and uncertainty associated…
Qiqing Tao, Sudip Sharma, Koichiro Tamura, Sudhir Kumar
The relative rate framework (RRF) can estimate divergence times from branch lengths in a phylogeny, which is the theoretical basis of the RelTime method frequently-applied, relaxed clock approach for molecular dating that scales well for large phylogenies. The use of RRF has also enabled the development of…
Jose Barba-Montoya, Qiqing Tao, Sudhir Kumar, Barbara Holland
Rapid relaxed-clock dating methods are frequently applied to analyze phylogenomic data sets containing hundreds to thousands of sequences because of their accuracy and computational efficiency. However, the relative performance of different rapid dating methods is yet to be compared on the same data sets, and, thus…
Gernot Münster
With this question the sixth chapter of Thomas Mann's "The Magic Mountain" begins: "What is time? A mystery – insubstantial and almighty. A prerequisite of the world of appearances, a motion, coupled and mingled with the being of bodies in space and their movement. But would there be no time, if there were no motion?…
Beatriz Mello, Qiqing Tao, Sudhir Kumar
Concurrent molecular dating of population and species divergences is essential in many biological investigations, including phylogeography, phylodynamics, and species delimitation studies. Multiple sequence alignments used in these investigations frequently consist of both intra- and inter-species samples (mixed…
Alan J S Beavan, Philip C J Donoghue, Mark A Beaumont, Davide Pisani + 1 more
'David T E Bryant'] Title: Abstract Relaxed molecular clock methods allow the use of genomic data to estimate divergence times across the tree of life. This is most commonly achieved in Bayesian analyses where the molecular clock is calibrated a priori through the integration of fossil information. Alternatively…
Sayaka Miura, Koichiro Tamura, Sergei L. Kosakovsky Pond, Louise A. Huuki + 3 more
Pathogen timetrees are phylogenies scaled to time. They reveal the temporal history of a pathogen spread through the populations as captured in the evolutionary history of strains. These timetrees are inferred by using molecular sequences of pathogenic strains sampled at different times. That is, temporally sampled…
K. L. H. Bryan, A. J. M. Medved
We investigate three aspects of the supposed problem of time: The disagreement between the treatments of time in general relativity and quantum theory, the problem of recovering time from within an isolated Universe and the prevalence of a unidirectional time flow (i.e., the so-called arrow of time). Under our…
Álvaro Mozota Frauca
In this paper I argue that the fundamental aspect of our notion of time is that it defines an order relation, be it a total order relation between configurations of the world or just a partial order relation between events. This position is in contrast with a relationalist view popular in the quantum gravity…
Claudio Borghi
This paper puts forward a broad critical analysis of the concept of physical time. Clock effect is conceived as a consequence of the variation of the gravitational or pseudo gravitational potential, and it is remarked that only some real clocks measure durations in agreement with the predictions of general relativity.…
Mario Radovan
The paper puts forward a conceptual framework in which the phenomenon of time can be presented and discussed in a proper way. We argue that change is ontologically and epistemologically a more basic phenomenon than time. Time is an abstract entity created by the human mind on the basis of the experience of change.…
M. Bauer, Cesar Augusto Aguillon, Gustavo Alberto Vivas García
The perspective is advanced that the time parameter in quantum mechanics corresponds to the time coordinate in a Minkowski flat spacetime local approximation to the actual dynamical curved spacetime of General Relativity, rather than to an external Newtonian reference frame. There is no incompatibility, as generally…
Umberto Lucia, Giulia Grisolia
Causality is the relationship between causes and effects. Following Relativity, any cause of an event must always be in the past light cone of the event itself, but causes and effect must always be related to some interactions. In this paper, causality is developed as a consequence of the analysis of the Einstein…
Plamen L. Simeonov
This paper presents yet another personal reflection on one the most important concepts in both science and the humanities: time. This elusive notion has been not only bothering philosophers since Plato and Aristotle. It goes throughout human history embracing all analytical and creative (anthropocentric) disciplines.…
Authors not listed
The equilibrium binding affinity has traditionally guided the drug discovery. Despite offering insight into the extent of binding, it is occasionally inaccurate in predicting biological response. Emerging evidence suggests that the lifetime of binary complex, known as residence time (RT), is more directly correlated…
Authors not listed
The residence time (τ) of a drug bound to a receptor target is increasingly recognized as a key property to control during ligand-optimization campaigns and provides a useful dimension for modulating compound profiles in addition to binding affinity. For this reason, many computational approaches have been developed to…