23 papers · ranked by Valyu relevance
Hervé Philippe, Henner Brinkmann, Dennis V. Lavrov, D. Timothy J. Littlewood + 4 more
Here, taking these three studies as a case in point, we discuss pitfalls that the simple addition of sequences cannot avoid, and show how the observed incongruence can be largely overcome and how improved bioinformatics methods can help reveal the full potential of phylogenomics. Two factors contribute significantly to…
Cheong Xin Chan, Mark A Ragan
Thanks to advances in next-generation technologies, genome sequences are now being generated at breadth (e.g. across environments) and depth (thousands of closely related strains, individuals or samples) unimaginable only a few years ago. Phylogenomics - the study of evolutionary relationships based on comparative…
Guillaume Bernard, Cheong Xin Chan, Yao-ban Chan, Xin-Yi Chua + 4 more
We are amidst an ongoing flood of sequence data arising from the application of high-throughput technologies, and a concomitant fundamental revision in our understanding of how genomes evolve individually and within the biosphere. Workflows for phylogenomic inference must accommodate data that are not only much larger…
Casey W. Dunn, Mark Howison, Felipe Zapata
Background: In the past decade, transcriptome data have become an important component of many phylogenetic studies. They are a cost-effective source of protein-coding gene sequences, and have helped projects grow from a few genes to hundreds or thousands of genes. Phylogenetic studies now regularly include genes from…
Hervé Philippe, Mathieu Blanchette
The First Phylogenomics Conference was held in Ste-Adèle (Québec, Canada) in March 2006. Selected papers appear in this special issue of BMC Evolutionary Biology. Here, we give an introduction to the field and provide an overview of the articles presented in this issue.
Michael D. Lee
Genome-level evolutionary inference (i.e., phylogenomics) is becoming an increasingly essential step in many biologists’ work - such as in the characterization of newly recovered genomes, or in leveraging available reference genomes to guide evolutionary questions. Accordingly, there are several tools available for the…
Alae-Eddine Sahbou, Driss Iraqi, Rachid Mentag, Slimane Khayi
Here we present the BuscoPhylo tool that enables both students and established scientists to easily perform Busco-based phylogenomic analysis starting from a set of genomes sequences. BuscoPhylo is an efficient and user-friendly web server freely accessible at [https://buscophylo.inra.org.ma/](). The source code, along…
Gustavo A. Bravo, Alexandre Antonelli, Christine D. Bacon, Krzysztof Bartoszek + 17 more
Building the Tree of Life (ToL) is a major challenge of modern biology, requiring advances in cyberinfrastructure, data collection, theory, and more. Here, we argue that phylogenomics stands to benefit by embracing the many heterogeneous genomic signals emerging from the first decade of large-scale phylogenetic…
Liang Liu, Zhenxiang Xi, Shaoyuan Wu, Charles C. Davis + 1 more
'Scott V. Edwards'] As researchers collect increasingly large molecular data sets to reconstruct the Tree of Life, the heterogeneity of signals in the genomes of diverse organisms poses challenges for traditional phylogenetic analysis. A class of phylogenetic methods known as 'species tree methods' have been proposed…
Sarah Teichman, Michael D. Lee, Amy D. Willis
Microbiome scientists critically need modern tools to explore and analyze microbial evolution. Often this involves studying the evolution of microbial genomes as a whole. However, different genes in a single genome can be subject to different evolutionary pressures, which can result in distinct gene-level evolutionary…
Julian R. Dupuis, Forest T. Bremer, Angela Kauwe, Michael San Jose + 3 more
High-throughput sequencing has fundamentally changed how molecular phylogenetic datasets are assembled, and phylogenomic datasets commonly contain 50-100-fold more loci than those generated using traditional Sanger-based approaches. Here, we demonstrate a new approach for building phylogenomic datasets using single…
Marc Hellmuth, Nicolas Wieseke, Marcus Lechner, Hans‐Peter Lenhof + 2 more
'Martin Middendorf' 'Peter F. Stadler'] Abstract. Phylogenomics heavily relies on well-curated sequence data sets that consist, for each gene, exclusively of 1:1-orthologous. Paralogs are treated as a dangerous nuisance that has to be detected and removed. We show here that this severe restriction of the data sets is…
Pablo Vinuesa, Luz Edith Ochoa-Sánchez, Bruno Contreras-Moreira
The massive accumulation of genome-sequences in public databases promoted the proliferation of genome-level phylogenetic analyses in many areas of biological research. However, due to diverse evolutionary and genetic processes, many loci have undesirable properties for phylogenetic reconstruction. These, if undetected…
Aurore Comte, Théo Tricou, Eric Tannier, Julien Joseph + 6 more
In phylogenomics, incongruences between gene trees, resulting from both artifactual and biological reasons, are known to decrease the signal-to-noise ratio and complicate species tree inference. The amount of data handled today in classical phylogenomic analyses precludes manual error detection and removal. However, a…
Roland Wittler
We present a new whole-genome based approach to infer large-scale phylogenies that is alignment- and reference-free. In contrast to other methods, it does not rely on pairwise comparisons to determine distances to infer edges in a tree. Instead, a colored de-Bruijn graph is constructed, and information on common…
P Natsidis, A Tsakogiannis, P Pavlidis, CS Tsigenopoulos + 1 more
Sparidae (Teleostei: Spariformes) are a family of fish constituted by approximately 150 species with high popularity and commercial value, such as porgies and seabreams. Although the phylogeny of this family has been investigated multiple times, its position among other teleost groups remains ambiguous. Most studies…
Ruriko Yoshida
- 1. Introduction - 2. Data Science Overview - (a) Supervised Learning (Inferential Statistics) - i. Classifications - ii. Regression - (b) Unsupervised Learning (Descriptive Statistics) - 3. Phylogenetics to Phylogenomics - (a) Phylogenetic Trees - (b) Space of Phylogenetic Trees - 4. Basics in Tropical Geometry - 5.…
Erfan Sayyari, James B. Whitfield, Siavash Mirarab
Phylogenomics has ushered in an age of discordance. Analyses often reveal abundant discordances among phylogenies of different parts of genomes, as well as incongruences between species trees obtained using different methods or data partitions. Researchers are often left trying to make sense of such incongruences.…
Dominique Sydow, Eva Aßmann, Albert J. Kooistra, Friedrich Rippmann + 1 more
Protein kinases are among the most important drug targets because their dysregulation can cause cancer, inflammatory, and degenerative diseases. Developing selective inhibitors is challenging due to the highly conserved binding sites across the roughly 500 human kinases. Thus, detecting subtle similarities on a…
Dariia Yehorova, Rory Crean, Peter Kasson, Shina Caroline Lynn Kamerlin
Protein structure (and thus function) is dictated by non-covalent interaction networks. These can be highly evolutionarily conserved across protein families, the members of which can diverge in sequence and evolutionary history. Here we present KIN, a tool to identify and analyze conserved non-covalent interaction…
Authors not listed
The rise of antibiotic resistance has necessitated the exploration of unconventional sources for novel antimicrobial agents. One emerging novel frontier is "de-extinct" molecules – bioactive peptides, antibiotics, and other bioactive agents reconstructed from ancient or extinct organisms – a groundbreaking convergence…
Zhiwen Pan, Jan Dellith, Lothar Wondraczek
Understanding the multivariate origin of physical properties is particularly complex for polyionic glasses. As a concept, the term genome has been used to describe the entirety of structure-property relations in solid materials, based on functional genes acting as descriptors for a particular property, for example, for…
Authors not listed
The new European (EU) regulation on water reuse explicitly incorporates antimicrobial resistance (AMR) into routine monitoring and risk management, creating an urgent need to define target antibiotic resistance genes (ARGs) for reclaimed irrigation water and agricultural sludge. However, existing global data largely…