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View article: Assessing phylogenetic confidence at pandemic scales
Assessing phylogenetic confidence at pandemic scales Open
Phylogenetics has a central role in evolutionary biology and genomic epidemiology 1 . Assessing phylogenetic confidence and reliability is therefore crucial and the methods that do this, such as those derived from Felsenstein’s bootstrap 2…
View article: piqtree: A Python Package for Seamless Phylogenetic Inference with IQ-TREE
piqtree: A Python Package for Seamless Phylogenetic Inference with IQ-TREE Open
piqtree is an easy to use, open-source Python package that directly exposes IQ-TREE’s phylogenetic inference engine. It offers Python functions for performing many of IQ-TREE’s capabilities including phylogenetic reconstruction, ultrafast …
View article: Refining Graduation Classification Accuracy with Synergistic Deep Learning Models
Refining Graduation Classification Accuracy with Synergistic Deep Learning Models Open
Learning Analytics plays an important role in monitoring and improving educational outcomes, but is often challenged by limited dataset sizes, resulting from privacy regulations and curriculum changes. This paper proposes the LATCGAd (Lear…
View article: IQ2MC: A New Framework to Infer Phylogenetic Time Trees Using IQ-TREE 3 and MCMCTree with Mixture Models
IQ2MC: A New Framework to Infer Phylogenetic Time Trees Using IQ-TREE 3 and MCMCTree with Mixture Models Open
IQ-TREE and MCMCTree are two widely used phylogenetic tools to infer phylogenetic trees and estimate divergence times, respectively. As MCMCTree performs fast approximate Markov Chain Monte Carlo sampling to obtain the times along a fixed …
View article: CORRELATION OF ELEMENTS ACCUMULATION IN ROOTS AND FRUIT OF BLACK PEPPER (Piper nigrum L.) UNDER ARSENIC SPECIES STRESS
CORRELATION OF ELEMENTS ACCUMULATION IN ROOTS AND FRUIT OF BLACK PEPPER (Piper nigrum L.) UNDER ARSENIC SPECIES STRESS Open
Sự ô nhiễm dạng asen trong đất nông nghiệp đe dọa sự sinh trưởng của cây trồng và an toàn thực phẩm, nhưng tác động của nó đến quá trình tích lũy dinh dưỡng trong cây vẫn chưa được hiểu rõ. Nghiên cứu này đánh giá sự tích lũy, vận chuyển v…
View article: IQ-TREE 3: Phylogenomic Inference Software using Complex Evolutionary Models
IQ-TREE 3: Phylogenomic Inference Software using Complex Evolutionary Models Open
IQ-TREE (http://www.iqtree.org) is a widely used open-source software tool for efficiently inferring phylogenetic trees under maximum likelihood. Here, we present IQ-TREE version 3, the third major release of the software. IQ-TREE 3 signif…
View article: Robust Phylogenetics
Robust Phylogenetics Open
We present a robust phylogenetic inference method, called the trimmed log-likelihood method, which effectively identifies fast-evolving, saturated, or erroneous sites in both simulated and empirical multiple sequence alignments. This metho…
View article: Real-Time Machine Learning-Based Physical Model for Estimating Photovoltaic Output Power Using Meteorological Data
Real-Time Machine Learning-Based Physical Model for Estimating Photovoltaic Output Power Using Meteorological Data Open
Accurately estimating the output power of photovoltaic (PV) systems is challenging because of missing meteorological data and variable environmental conditions. This paper introduces a novel approach for the real-time estimation of PV outp…
View article: MixtureFinder: Estimating DNA Mixture Models for Phylogenetic Analyses
MixtureFinder: Estimating DNA Mixture Models for Phylogenetic Analyses Open
In phylogenetic studies, both partitioned models and mixture models are used to account for heterogeneity in molecular evolution among the sites of DNA sequence alignments. Partitioned models require the user to specify the grouping of sit…
View article: TreeFormer: A transformer-based tree rearrangement operation for phylogenetic reconstruction
TreeFormer: A transformer-based tree rearrangement operation for phylogenetic reconstruction Open
Phylogenetic inference is a fundamental problem in biology, which studies the origins and evolutionary relationships among species. Popular phylogenetic inference methods, such as IQ-TREE, RAxML, and PHYML, typically utilize heuristic tree…
View article: This is SPRTA: assessing phylogenetic confidence at pandemic scales
This is SPRTA: assessing phylogenetic confidence at pandemic scales Open
Phylogenetics plays a central role in evolutionary biology and genomic epidemiology. Assessing phylogenetic confidence and reliability is therefore crucial and methods to do this, such as Felsenstein’s bootstrap, are among the most used in…
View article: A robustly rooted tree of eukaryotes reveals their excavate ancestry.
A robustly rooted tree of eukaryotes reveals their excavate ancestry. Open
The eukaryote Tree of Life (eToL) depicts the relationships among all eukaryotic organisms; its root represents the last eukaryotic common ancestor (LECA) from which all extant complex lifeforms are descended. Locating this root is crucial…
View article: CMAPLE: Efficient Phylogenetic Inference in the Pandemic Era
CMAPLE: Efficient Phylogenetic Inference in the Pandemic Era Open
We have recently introduced MAPLE (MAximum Parsimonious Likelihood Estimation), a new pandemic-scale phylogenetic inference method exclusively designed for genomic epidemiology. In response to the need for enhancing MAPLE's performance and…
View article: CMAPLE: efficient phylogenetic inference in the pandemic era
CMAPLE: efficient phylogenetic inference in the pandemic era Open
We have recently introduced MAPLE (MAximum Parsimonious Likelihood Estimation), a new pandemic-scale phylogenetic inference method exclusively designed for genomic epidemiology. In response to the need for enhancing MAPLE's performance and…
View article: Order of amino acid recruitment into the genetic code resolved by Last Universal Common Ancestor’s protein domains
Order of amino acid recruitment into the genetic code resolved by Last Universal Common Ancestor’s protein domains Open
The current “consensus” order in which amino acids were added to the genetic code is based on potentially biased criteria such as absence of sulfur-containing amino acids from the Urey-Miller experiment which lacked sulfur. Even if inferre…
View article: MixtureFinder: Estimating DNA mixture models for phylogenetic analyses
MixtureFinder: Estimating DNA mixture models for phylogenetic analyses Open
In phylogenetic studies, both partitioned models and mixture models are used to account for heterogeneity in molecular evolution among the sites of DNA sequence alignments. Partitioned models require the user to specify the grouping of sit…
View article: AliSim-HPC: parallel sequence simulator for phylogenetics
AliSim-HPC: parallel sequence simulator for phylogenetics Open
Motivation Sequence simulation plays a vital role in phylogenetics with many applications, such as evaluating phylogenetic methods, testing hypotheses, and generating training data for machine-learning applications. We recently introduced …
View article: <i>Atractylodes macrocephala</i> Rhizomes Contain Anti-inflammatory Sesquiterpenes
<i>Atractylodes macrocephala</i> Rhizomes Contain Anti-inflammatory Sesquiterpenes Open
Two new compounds, named eudesm-4(15),7-diene-3α,9β,11-triol (1) and eudesm-4(15),7-diene-1β,3α,9β,11-tetraol (2) together with three known sesquiterpene lactones (1S,5R,7R,10R)-secoatractylolactone (3), (1S,5R,7R,10R)-secoatractylolactone…
View article: AliSim-HPC: parallel sequence simulator for phylogenetics
AliSim-HPC: parallel sequence simulator for phylogenetics Open
Motivation Sequence simulation plays a vital role in phylogenetics with many applications, such as evaluating phylogenetic methods, testing hypotheses, and generating training data for machine-learning applications. We recently introduced …
View article: 2022 Zuckerkandl Prize
2022 Zuckerkandl Prize Open
View article: MAST: Phylogenetic Inference with Mixtures Across Sites and Trees
MAST: Phylogenetic Inference with Mixtures Across Sites and Trees Open
Hundreds or thousands of loci are now routinely used in modern phylogenomic studies. Concatenation approaches to tree inference assume that there is a single topology for the entire dataset, but different loci may have different evolutiona…
View article: Updated site concordance factors minimize effects of homoplasy and taxon sampling
Updated site concordance factors minimize effects of homoplasy and taxon sampling Open
Motivation Site concordance factors (sCFs) have become a widely used way to summarize discordance in phylogenomic datasets. However, the original version of sCFs were calculated by sampling a quartet of tip taxa and then applying parsimony…
View article: DecentTree: Scalable Neighbour-Joining for the Genomic Era
DecentTree: Scalable Neighbour-Joining for the Genomic Era Open
Summary Neighbour-Joining is one of the most widely used distance-based phylogenetic inference methods. However, current implementations do not scale well for datasets with more than 10,000 sequences. Given the increasing pace of generatin…
View article: Investigation of xanthine oxidase inhibitors in bioactive components of Jatropha podagrica stem bark
Investigation of xanthine oxidase inhibitors in bioactive components of Jatropha podagrica stem bark Open
This study was conducted to examine the activity of antioxidants against xanthine oxidase in bioactive extracts from Jatropha podagrica stem bark. Among the extracts, the EtOAc extract showed the strongest antioxidant activity and xanthine…
View article: Maximum likelihood pandemic-scale phylogenetics
Maximum likelihood pandemic-scale phylogenetics Open
Summary Phylogenetics plays a crucial role in the interpretation of genomic data 1 . Phylogenetic analyses of SARS-CoV-2 genomes have allowed the detailed study of the virus’s origins 2 , of its international 3,4 and local 4–9 spread, and …
View article: nQMaker: Estimating Time Nonreversible Amino Acid Substitution Models
nQMaker: Estimating Time Nonreversible Amino Acid Substitution Models Open
Amino acid substitution models are a key component in phylogenetic analyses of protein sequences. All commonly used amino acid models available to date are time-reversible, an assumption designed for computational convenience but not for b…
View article: AliSim: A Fast and Versatile Phylogenetic Sequence Simulator For the Genomic Era
AliSim: A Fast and Versatile Phylogenetic Sequence Simulator For the Genomic Era Open
Sequence simulators play an important role in phylogenetics. Simulated data has many applications, such as evaluating the performance of different methods, hypothesis testing with parametric bootstraps, and, more recently, generating data …
View article: nQMaker: estimating time non-reversible amino acid substitution models
nQMaker: estimating time non-reversible amino acid substitution models Open
Amino acid substitution models are a key component in phylogenetic analyses of protein sequences. All amino acid models available to date are time-reversible, an assumption designed for computational convenience but not for biological real…
View article: A Comprehensive Phylogenetic Analysis of the Serpin Superfamily
A Comprehensive Phylogenetic Analysis of the Serpin Superfamily Open
Serine protease inhibitors (serpins) are found in all kingdoms of life and play essential roles in multiple physiological processes. Owing to the diversity of the superfamily, phylogenetic analysis is challenging and prokaryotic serpins ha…
View article: QMaker: Fast and Accurate Method to Estimate Empirical Models of Protein Evolution
QMaker: Fast and Accurate Method to Estimate Empirical Models of Protein Evolution Open
Amino acid substitution models play a crucial role in phylogenetic analyses. Maximum likelihood (ML) methods have been proposed to estimate amino acid substitution models; however, they are typically complicated and slow. In this article, …