Article
Biochemical Research Methods
Momoko Hayamizu, Kazuhisa Makino
Summary: Tree-based phylogenetic networks are a powerful model for representing complex data or non-tree-like evolution. However, these networks can have exponentially many support trees, leading to various computational problems. Hayamizu recently proposed a structure theorem and provided linear-time and linear-delay algorithms for different problems. In this paper, we focus on ranking the top-k support trees of a tree-based phylogenetic network based on their likelihood values, and present a linear-delay (optimal) algorithm for this problem.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
(2023)
Article
Biochemical Research Methods
Ben Bettisworth, Alexandros Stamatakis
Summary: RootDigger is a software that uses a non-reversible Markov model to compute the most likely root location and infer confidence values for each possible root placement on a tree. It is successful at finding roots and occasionally outperforms similar tools like IQ-TREE and MAD. The exhaustive mode of RootDigger helps in quantifying and explaining uncertainty in rooting positions.
BMC BIOINFORMATICS
(2021)
Article
Biochemical Research Methods
Eleanor Wedell, Yirong Cai, Tandy Warnow
Summary: SCAMPP is a technique that extends the scalability of likelihood-based phylogenetic placement methods to ultra-large backbone trees, achieving accurate evolutionary tree classification. It can handle ultra-large backbone trees with 50,000 or more leaves and has higher accuracy compared to other fast phylogenetic placement methods.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
(2023)
Article
Plant Sciences
A. Baradar, A. Hosseini, C. Ratti, S. Hosseini
Summary: To accurately classify BYMV, comparing full genome sequences is crucial rather than relying on partial sequences or individual genes. Nuclear inclusion proteins a and b (NIa and NIb) along with viral protein genome linked (VPg) were identified as suitable evolutionary markers for phylogenetic studies. The study demonstrated 10 main monophyletic clades of BYMV strains which showed consistency with recent phylogenetic studies based on whole genome sequences.
PHYSIOLOGICAL AND MOLECULAR PLANT PATHOLOGY
(2021)
Article
Mathematics, Applied
Mirko Wilde, Mareike Fischer
Summary: Phylogenetic trees are commonly used to model evolution. This manuscript presents new findings on the relationship between the maximum parsimony method and the definition of phylogenetic trees. The study shows that the set of characters with parsimony score k can uniquely define a binary phylogenetic tree T with n > 4k leaves. Additionally, the research expands this understanding to identify the range of n values for which trees sharing the same A(k)-alignment can exist. The study also highlights the relationship between the nearest neighbor interchange operation and the uniqueness of the A(k)-alignment.
DISCRETE APPLIED MATHEMATICS
(2023)
Article
Biochemistry & Molecular Biology
Sudip Sharma, Sudhir Kumar
Summary: The study discovers that using subsample-upsample approach can significantly reduce the computational costs in analyzing long sequence alignments in molecular evolution, while still recovering the correct optimal substitution model. An adaptive protocol called ModelTamer is proposed, which can select the optimal models in much shorter time and with much less memory usage.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
Benoit Morel, Paul Schade, Sarah Lutteropp, Tom A. Williams, Gergely J. Szollosi, Alexandros Stamatakis
Summary: SpeciesRax is a maximum likelihood method that can infer a rooted species tree from a set of gene family trees and can account for gene duplication, loss, and transfer events. It leverages the phylogenetic rooting signal in gene trees and infers species tree branch lengths and support values through paralogy-aware quartets extracted from the gene family trees. It is faster and at least as accurate as the best competing methods.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Ecology
Rui Borges, Bastien Boussau, Sebastian Hoehna, Ricardo J. Pereira, Carolin Kosiol
Summary: The availability of population genomic data through new sequencing technologies provides unprecedented opportunities for estimating important evolutionary forces. However, analytical methods that can handle sequence divergence and polymorphisms are rare and not easily accessible. We developed a new method (PoMos) that can handle both scenarios and applied it to study the phylogenetic relationships of grasshoppers.
METHODS IN ECOLOGY AND EVOLUTION
(2022)
Article
Biochemical Research Methods
Sarah Lutteropp, Celine Scornavacca, Alexey M. Kozlov, Benoit Morel, Alexandros Stamatakis
Summary: NetRAX is a tool for maximum likelihood inference of phylogenetic networks in the absence of incomplete lineage sorting. It efficiently computes the phylogenetic likelihood function on trees and extends them to phylogenetic networks. The tool can infer ML phylogenetic networks from partitioned multiple sequence alignments and provides the results in Extended Newick format.
Article
Mathematics
Fouzul Atik, M. Rajesh Kannan, Ravindra B. Bapat
Summary: The article discusses the relationship between weighted trees and distance matrices, including the connection between the rank of the weighted Laplacian matrix and trees, the necessary and sufficient conditions for the invertibility of the distance matrix with matrix weights, and some properties of the distance matrices of matrix weighted trees. Finally, it derives an interlacing inequality for the eigenvalues of distance and Laplacian matrices when using positive definite matrix weights.
LINEAR & MULTILINEAR ALGEBRA
(2021)
Article
Multidisciplinary Sciences
Sonia Trujillo-Argueta, Rafael F. del Castillo, Abril Velasco-Murguia
Summary: DNA-barcoding is a useful tool for species identification, although its efficacy for plants still needs to be studied. By analyzing rbcLa sequences in tropical cloud forest vascular plants, it was found that ML tree-based analysis is the most effective method for species discrimination.
Article
Statistics & Probability
Jean Feng, William S. DeWitt, Aaron McKenna, Noah Simon, Amy D. Willis, Frederick A. Matsen
Summary: CRISPR technology enables cell lineage tracing in complex multicellular organisms by using insertion-deletion mutations of synthetic genomic barcodes. Researchers have proposed a statistical model and developed a procedure to estimate tree topology, branch lengths, and mutation parameters. Their method infers relative ordering across parallel lineages, offering advantages over existing techniques.
ANNALS OF APPLIED STATISTICS
(2021)
Article
Biology
M. K. Garba, T. M. W. Nye, J. Lueg, S. F. Huckemann
Summary: The paper introduces a new space of phylogenetic trees called wald space, motivated by the need for a space suitable for statistical analysis of phylogenies with a geometry based on biologically principled assumptions. It investigates two related geometries on wald space involving Fisher information metric and continuous-valued Gaussian process. Computational methods are derived to compute geodesics in polynomial time for both geometries and numerical results show their similarity. The canonical and biologically motivated space proposed in the study is shown to be substantially different from the BHV geometry.
JOURNAL OF MATHEMATICAL BIOLOGY
(2021)
Article
Biochemical Research Methods
Matthew O. Macaulay, Aaron Darling, Mathieu O. Fourment
Summary: Bayesian inference is widely used in phylogenetics to compute distributions of phylogenies. This paper explores the use of hyperbolic space as a low dimensional representation for tree-like data. The authors embed genomic sequences in hyperbolic space and perform hyperbolic Markov Chain Monte Carlo for Bayesian inference. They demonstrate the effectiveness of this method on eight data sets and investigate the impact of embedding dimension and hyperbolic curvature on performance. The results show that hyperbolic space is suitable for phylogenetic inference.
PLOS COMPUTATIONAL BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Alessio Caminata, Noah Giansiracusa, Han-Bom Moon, Luca Schaffler
Summary: Researchers successfully demonstrate that weighted dissimilarity vectors form a tropical subvariety of the tropical Grassmannian by replacing the definition of the dissimilarity map, providing a geometric interpretation in terms of configurations of points on rational normal curves.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)