Koichiro Tamura
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View article: Evolutionary sparse learning reveals the shared genetic basis of convergent traits
Evolutionary sparse learning reveals the shared genetic basis of convergent traits Open
Cases abound in which nearly identical traits have appeared in distant species facing similar environments. These unmistakable examples of adaptive evolution offer opportunities to gain insight into their genetic origins and mechanisms thr…
View article: R3F: An R package for evolutionary dates, rates, and priors using the relative rate framework.
R3F: An R package for evolutionary dates, rates, and priors using the relative rate framework. Open
The source codes and related instructions for installing and implementing R3F are available from GitHub (https://github.com/cathyqqtao/R3F).
View article: Evolutionary sparse learning with paired species contrast reveals the shared genetic basis of convergent traits
Evolutionary sparse learning with paired species contrast reveals the shared genetic basis of convergent traits Open
Cases abound in which nearly identical traits have appeared in distant species facing similar environments. These unmistakable examples of adaptive evolution offer opportunities to gain insight into their genetic origins and mechanisms thr…
View article: MEGA12: Molecular Evolutionary Genetic Analysis version 12 for adaptive and green computing
MEGA12: Molecular Evolutionary Genetic Analysis version 12 for adaptive and green computing Open
We introduce the 12th version of the Molecular Evolutionary Genetics Analysis ( MEGA ) software. This latest version brings many significant improvements by reducing the computational time needed for selecting optimal substitution models a…
View article: MEGA12: Molecular Evolutionary Genetic Analysis Version 12 for Adaptive and Green Computing
MEGA12: Molecular Evolutionary Genetic Analysis Version 12 for Adaptive and Green Computing Open
We introduce the 12th version of the Molecular Evolutionary Genetics Analysis (MEGA12) software. This latest version brings many significant improvements by reducing the computational time needed for selecting optimal substitution models a…
View article: Computational Reproducibility of Molecular Phylogenies
Computational Reproducibility of Molecular Phylogenies Open
Repeated runs of the same program can generate different molecular phylogenies from identical data sets under the same analytical conditions. This lack of reproducibility of inferred phylogenies casts a long shadow on downstream research e…
View article: Shared evolutionary trajectories of three independent neo-sex chromosomes in <i>Drosophila</i>
Shared evolutionary trajectories of three independent neo-sex chromosomes in <i>Drosophila</i> Open
Dosage compensation (DC) on the X Chromosome counteracts the deleterious effects of gene loss on the Y Chromosome. However, DC is not efficient if the X Chromosome also degenerates. This indeed occurs in Drosophila miranda , in which both …
View article: MEGA11: Molecular Evolutionary Genetics Analysis Version 11
MEGA11: Molecular Evolutionary Genetics Analysis Version 11 Open
The Molecular Evolutionary Genetics Analysis (MEGA) software has matured to contain a large collection of methods and tools of computational molecular evolution. Here, we describe new additions that make MEGA a more comprehensive tool for …
View article: Evolutionary trajectories of three independent neo-sex chromosomes in<i>Drosophila</i>
Evolutionary trajectories of three independent neo-sex chromosomes in<i>Drosophila</i> Open
Dosage compensation (DC) on the X chromosome is a mechanism to counteract the deleterious effects by gene loss from the Y chromosome. However, DC cannot work efficiently if the X chromosome also degenerates. This indeed occurs in the neo-s…
View article: Modeling and Analysis of Effects on Financial Markets from Influence Relationships in Social Media.
Modeling and Analysis of Effects on Financial Markets from Influence Relationships in Social Media. Open
The data of social media has received much attention to observe and predict real-world events. For example, It is used to predict financial markets, products demand, and voter turnout. While these works regards social media as a sensor of …
View article: PathFinder: Bayesian inference of clone migration histories in cancer
PathFinder: Bayesian inference of clone migration histories in cancer Open
Summary Metastases cause a vast majority of cancer morbidity and mortality. Metastatic clones are formed by dispersal of cancer cells to secondary tissues, and are not medically detected or visible until later stages of cancer development.…
View article: PathFinder: Bayesian inference of clone migration histories in cancer
PathFinder: Bayesian inference of clone migration histories in cancer Open
Summary Metastases form by dispersal of cancer cells to secondary tissues. They cause a vast majority of cancer morbidity and mortality. Metastatic clones are not medically detected or visible until later stages of cancer development. Thus…
View article: A new method for inferring timetrees from temporally sampled molecular sequences
A new method for inferring timetrees from temporally sampled molecular sequences Open
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 …
View article: Molecular Evolutionary Genetics Analysis (MEGA) for macOS
Molecular Evolutionary Genetics Analysis (MEGA) for macOS Open
The Molecular Evolutionary Genetics Analysis (MEGA) software enables comparative analysis of molecular sequences in phylogenetics and evolutionary medicine. Here, we introduce the macOS version of the MEGA software. This new version elimin…
View article: Reliable Confidence Intervals for RelTime Estimates of Evolutionary Divergence Times
Reliable Confidence Intervals for RelTime Estimates of Evolutionary Divergence Times Open
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 evolutiona…
View article: Reliable confidence intervals for RelTime estimates of evolutionary divergence times
Reliable confidence intervals for RelTime estimates of evolutionary divergence times Open
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 evolutiona…
View article: A new method for inferring timetrees from temporally sampled molecular sequences
A new method for inferring timetrees from temporally sampled molecular sequences Open
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 …
View article: A Machine Learning Method for Detecting Autocorrelation of Evolutionary Rates in Large Phylogenies
A Machine Learning Method for Detecting Autocorrelation of Evolutionary Rates in Large Phylogenies Open
New species arise from pre-existing species and inherit similar genomes and environments. This predicts greater similarity of the tempo of molecular evolution between direct ancestors and descendants, resulting in autocorrelation of evolut…
View article: A new method for detecting autocorrelation of evolutionary rates in large phylogenies
A new method for detecting autocorrelation of evolutionary rates in large phylogenies Open
New species arise from pre-existing species and inherit similar genomes and environments. This predicts greater similarity of mutation rates and the tempo of molecular evolution between direct ancestors and descendants, resulting in autoco…
View article: RelTime Relaxes the Strict Molecular Clock throughout the Phylogeny
RelTime Relaxes the Strict Molecular Clock throughout the Phylogeny Open
The RelTime method estimates divergence times when evolutionary rates vary among lineages. Theoretical analyses show that RelTime relaxes the strict molecular clock throughout a molecular phylogeny, and it performs well in the analyses of …
View article: Adaptive Landscape of Protein Variation in Human Exomes
Adaptive Landscape of Protein Variation in Human Exomes Open
The human genome contains hundreds of thousands of missense mutations. However, only a handful of these variants are known to be adaptive, which implies that adaptation through protein sequence change is an extremely rare phenomenon in hum…
View article: MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms
MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms Open
The Molecular Evolutionary Genetics Analysis (Mega) software implements many analytical methods and tools for phylogenomics and phylomedicine. Here, we report a transformation of Mega to enable cross-platform use on Microsoft Windows and L…
View article: Theoretical Foundation of the RelTime Method for Estimating Divergence Times from Variable Evolutionary Rates
Theoretical Foundation of the RelTime Method for Estimating Divergence Times from Variable Evolutionary Rates Open
RelTime estimates divergence times by relaxing the assumption of a strict molecular clock in a phylogeny. It shows excellent performance in estimating divergence times for both simulated and empirical molecular sequence data sets in which …
View article: Adaptive landscape of protein variation in human exomes
Adaptive landscape of protein variation in human exomes Open
The human genome contains hundreds of thousands of missense mutations. However, only a handful of these variants are known to be adaptive, which implies that adaptation through protein sequence change is an extremely rare phenomenon in hum…
View article: Model for Evaluation of Stock Values by Ensemble Model Using Deep Learning
Model for Evaluation of Stock Values by Ensemble Model Using Deep Learning Open
In order to encourage individual asset flow into the Japanese market through long-term investments, it is important to evaluate stock values of companies because stock prices of companies are determined not only by internal values, which a…
View article: Application of AMP Collectors in Nairobi CBD for Transport Planning
Application of AMP Collectors in Nairobi CBD for Transport Planning Open
This report gives a summary of the Anonymous MAC-address Packet (AMP) collector and its system installed in Nairobi in 2017, for the purpose of collecting unique Media Access Control (MAC) addresses emitted from Wi-Fi emitting devices to d…
View article: RelTime relaxes the strict molecular clock throughout the phylogeny
RelTime relaxes the strict molecular clock throughout the phylogeny Open
The RelTime method estimates divergence times when evolutionary rates vary among lineages. Theoretical analyses show that RelTime relaxes the strict molecular clock throughout a molecular phylogeny, and it performs well in the analysis of …
View article: Theoretical foundation of the RelTime method for estimating divergence times from variable evolutionary rates
Theoretical foundation of the RelTime method for estimating divergence times from variable evolutionary rates Open
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 …