A5068432987- Genomics and Phylogenetic Studies
- Genetic diversity and population structure
- Evolution and Paleontology Studies
- Plant and animal studies
- Biomedical Text Mining and Ontologies
- Plant Diversity and Evolution
- Ecology and Vegetation Dynamics Studies
- Computational Physics and Python Applications
- Chromosomal and Genetic Variations
- Machine Learning in Materials Science
- Genetics, Bioinformatics, and Biomedical Research
- Metal-Catalyzed Oxygenation Mechanisms
- Cognitive Abilities and Testing
- Gene expression and cancer classification
- Genetic Mapping and Diversity in Plants and Animals
- Quantum, superfluid, helium dynamics
- Mycorrhizal Fungi and Plant Interactions
- Child and Animal Learning Development
- Microbial Community Ecology and Physiology
- Advanced Chemical Physics Studies
- Memory and Neural Mechanisms
- Photosynthetic Processes and Mechanisms
- Genome Rearrangement Algorithms
Max Perutz Labs
2014-2024
Medical University of Vienna
2016-2024
Karlsruhe Institute of Technology
2019
Heidelberg Institute for Theoretical Studies
2019
University of Vienna
2014-2017
University of L'Aquila
2012
Abstract IQ-TREE (http://www.iqtree.org, last accessed February 6, 2020) is a user-friendly and widely used software package for phylogenetic inference using maximum likelihood. Since the release of version 1 in 2014, we have continuously expanded to integrate plethora new models sequence evolution efficient computational approaches deal with genomic data. Here, describe notable features 2 highlight key advantages over other software.
The standard bootstrap (SBS), despite being computationally intensive, is widely used in maximum likelihood phylogenetic analyses. We recently proposed the ultrafast approximation (UFBoot) to reduce computing time while achieving more unbiased branch supports than SBS under mild model violations. UFBoot has been steadily adopted as an efficient alternative and other approaches. Here, we present UFBoot2, which substantially accelerates reduces risk of overestimating due polytomies or severe...
In phylogenomics the analysis of concatenated gene alignments, so-called supermatrix, is commonly accompanied by assumption partition models. Under such models each gene, or more generally partition, allowed to evolve under its own evolutionary model. Although provide a comprehensive supermatrices, missing data may hamper tree search algorithms due existence phylogenetic (partial) terraces. Here, we introduce terrace aware (PTA) structure for efficient presence PTA exploits terraces and...
Abstract IQ-TREE ( http://www.iqtree.org ) is a user-friendly and widely used software package for phylogenetic inference using maximum likelihood. Since the release of version 1 in 2014, we have continuously expanded to integrate plethora new models sequence evolution efficient computational approaches deal with genomic data. Here, describe notable features 2 highlight key advantages over other software.
Abstract The standard bootstrap (SBS), despite being computationally intensive, is widely used in maximum likelihood phylogenetic analyses. We recently proposed the ultrafast approximation (UFBoot) to reduce computing time while achieving more unbiased branch supports than SBS under mild model violations. UFBoot has been steadily adopted as an efficient alternative and other approaches. Here, we present UFBoot2, which substantially accelerates reduces risk of overestimating due polytomies or...
Summary Phylogenetic diversity ( PD ) is a measure of biodiversity based on the evolutionary history species. Here, we discuss several optimization problems related to use , and more general split SD ), in conservation prioritization. Depending goal information available about species, one can construct routines that incorporate various constraints. We demonstrate how this be used select sets species for action. Specifically, species' geographic distributions, choice candidates under...
We used Quantum Monte Carlo (QMC) methods to study the polarizability and quadrupole moment of ethyne molecule using Jastrow-Antisymmetrised Geminal Power (JAGP) wave function, a compact strongly correlated variational ansatz. The compactness functional form full optimization all its parameters, including linear exponential coefficients in atomic orbitals, allow us observe fast convergence electrical properties with size Jastrow basis sets. Both results on isotropic based Gaussian type...
In phylogenomic analysis the collection of trees with identical score (maximum likelihood or parsimony score) may hamper tree search algorithms. Such collections are coined phylogenetic terraces. For sparse supermatrices a lot missing data, number terraces and on can be very large. If not taken into account, computation time might unnecessarily spent to evaluate many that in fact have score. To save during search, it is worthwhile quickly identify such cases. The species sum scores for all...
Light-dependent protochlorophyllide oxidoreductase (LPOR) and dark-operative are evolutionary structurally distinct enzymes that essential for the synthesis of (bacterio)chlorophyll, primary pigment needed both anoxygenic oxygenic photosynthesis. In contrast to long-held hypothesis LPORs only present in phototrophs, we recently identified a functional LPOR aerobic phototrophic bacterium (AAPB) Dinoroseobacter shibae attributed its presence single horizontal gene transfer event from...
The brains and minds of our human ancestors remain inaccessible for experimental exploration. Therefore, we reconstructed cognitive evolution by projecting nonsynonymous/synonymous rate ratios (ω values) in mammalian phylogeny onto the anatomically modern (AMH) brain. This atlas retraces neurogenetic selection allows imputation ancestral task-related functional networks (FNs). Adaptive (high ω is associated with excitatory neurons synaptic function. It shifted from FNs motor control...
Abstract For a set of binary unrooted subtrees generating all trees compatible with them, i.e. their stand, is one the classical problems in phylogenetics. Here, we introduce Gentrius – an efficient algorithm to tackle this task. The has direct application practice. Namely, generates phylogenetic terraces - topologically distinct, equally scoring due missing data. Despite stand generation being computationally intractable, showed on simulated and biological datasets that stands millions...
A bstract Terraces in phylogenetic tree space are, among other things, important for the design of search strategies. While phenomenon terraces is already known unlinked partition models on partitioned phylogenomic data sets, it has not yet been studied if an analogous structure present under linked and scaled models. To this end, we analyze aspects such as log-likelihood distributions, likelihood-based significance tests, nearest neighborhood interchanges trees residing a terrace compare...
One approach in phylogenomics to infer the tree of life is based on concatenated multiple sequence alignments from many genes. Unfortunately, resulting so-called supermatrix usually sparse, that is, not every gene available for all species supermatrix. Due missing information a phylogenetic inference, assuming each evolves with its own substitution model, suffers terraces which trees show same likelihood. Here, we propose terrace aware (PTA) data structure efficient inference under partition...
Abstract Phylogenetic trees are routinely built from huge and yet incomplete multi-locus datasets often leading to phylogenetic terraces – topologically distinct equally scoring trees, which induce the same set of per locus subtrees. As typical tree inference software outputs only a single tree, identifying all with identical score challenges phylogenomics. Generating terrace requires constructing so-called stand for corresponding induced Here, we introduce Gentrius an efficient algorithm...
Multi-locus datasets are frequently used to infer phylogenies instead of using single locus. Missing data constitute a common challenge in such as they can lead stands, that is, sets trees compatible with the incomplete per-locus trees. Under many criteria from one stand have identical score. Hence, identifying stands and determining their sizes is crucial importance for robust phylogenetic analysis. Recently, Chernomor et al. published Gentrius, branch-and-bound algorithm enumerates all...