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Improving the efficiency of SPR moves in phylogenetic tree search methods based on maximum likelihood
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
inferredcites →https://doi.org/10.1002/0471650129.dob0522openalex-snapshot
PAUP * [Phylogenetic Analysis Using Parsimony (and Other Methods)]
inferredcites →https://doi.org/10.1002/9780471650126.dob0049.pub2openalex-snapshot
BAMBE (Bayesian Analysis in Molecular Biology and Evolution)
inferredcites →https://doi.org/10.1002/9780471650126.dob0534.pub2openalex-snapshot
PHYLIP ( PHYLogeny Inference Package)
inferredcites →https://doi.org/10.1007/11415770_23openalex-snapshot
Maximum Likelihood of Evolutionary Trees Is Hard
inferredcites →https://doi.org/10.1007/978-3-642-58250-9openalex-snapshot
Data Analysis: Scientific Modeling and Practical Application
inferredcites →https://doi.org/10.1007/978-3-642-58250-9_13openalex-snapshot
Evidence for a Relationship Between Algorithmic Scheme and Shape of Inferred Trees
inferredcites →https://doi.org/10.1007/bf00160154openalex-snapshot
Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods
inferredcites →https://doi.org/10.1007/bf01734359openalex-snapshot
Evolutionary trees from DNA sequences: A maximum likelihood approach
inferredcites →https://doi.org/10.1007/bf02109483openalex-snapshot
Maximum likelihood inference of protein phylogeny and the origin of chloroplasts
inferredcites →https://doi.org/10.1007/bf02338839openalex-snapshot
Probability Distribution of Molecular Evolutionary Trees: A New Method of Phylogenetic Inference
inferredcites →https://doi.org/10.1007/s002390010065openalex-snapshot
Direct Calculation of a Tree Length Using a Distance Matrix
inferredcites →https://doi.org/10.1016/s0304-3975(99)00235-2openalex-snapshot
Inferring evolutionary trees with strong combinatorial evidence
inferredcites →https://doi.org/10.1073/pnas.162224399openalex-snapshot
The metapopulation genetic algorithm: An efficient solution for the problem of large phylogeny estimation
inferredcites →https://doi.org/10.1080/10635150117772openalex-snapshot
Stochastic Search Strategy for Estimation of Maximum Likelihood Phylogenetic Trees
inferredcites →https://doi.org/10.1080/106351501750107413openalex-snapshot
Stochastic Search Strategy for Estimation of Maximum Likelihood Phylogenetic Trees
inferredcites →https://doi.org/10.1080/10635150390235520openalex-snapshot
A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood
inferredcites →https://doi.org/10.1080/10635150590905867openalex-snapshot
Phylogeny and Biogeography of Exacum (Gentianaceae): A Disjunctive Distribution in the Indian Ocean Basin Resulted from Long Distance Dispersal and Extensive Radiation
inferredcites →https://doi.org/10.1080/10635150590906028openalex-snapshot
Exploring Rate Variation Among and Within Sites in a Densely Sampled Tree: Species Level Phylogenetics of North American Tiger Beetles (Genus Cicindela)
inferredcites →https://doi.org/10.1080/10635150590906046openalex-snapshot
Biogeographic Interpretation of Splits Graphs: Least Squares Optimization of Branch Lengths
inferredcites →https://doi.org/10.1080/10635150590910249openalex-snapshot
Is Homoplasy or Lineage Sorting the Source of Incongruent mtDNA and Nuclear Gene Trees in the Stiff-Tailed Ducks (Nomonyx-Oxyura)?
inferredcites →https://doi.org/10.1089/106652702761034136openalex-snapshot
Fast and Accurate Phylogeny Reconstruction Algorithms Based on the Minimum-Evolution Principle
inferredcites →https://doi.org/10.1093/bioinformatics/10.1.41openalex-snapshot
fastDNAml: a tool for construction of phylogenetic trees of DNA sequences using maximum likelihood
inferredcites →https://doi.org/10.1093/bioinformatics/17.8.754openalex-snapshot
MRBAYES: Bayesian inference of phylogenetic trees
inferredcites →https://doi.org/10.1093/bioinformatics/bti191openalex-snapshot
RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees
inferredcites →https://doi.org/10.1093/molbev/msh176openalex-snapshot
IQPNNI: Moving Fast Through Tree Space and Stopping in Time
inferredcites →https://doi.org/10.1093/oso/9780198566106.001.0001openalex-snapshot
Mathematics of Evolution and Phylogeny
inferredcites →https://doi.org/10.1093/oso/9780198566106.003.0001openalex-snapshot
The Minium: Evolution Distance-Based Approach To Phylogenetic Inference
inferredcites →https://doi.org/10.1093/oso/9780198566106.003.0002openalex-snapshot
Likelihood Calculation in Molecular Phylogenetics
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a003969openalex-snapshot
Traditional Phylogenetic Reconstruction Methods Reconstruct Shallow and Deep Evolutionary Relationships Equally Well
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a004019openalex-snapshot
Improvement of Distance-Based Phylogenetic Methods by a Local Maximum Likelihood Approach Using Triplets
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a025924openalex-snapshot
A genetic algorithm for maximum-likelihood phylogeny inference using nucleotide sequence data
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a026160openalex-snapshot
Markov Chasin Monte Carlo Algorithms for the Bayesian Analysis of Phylogenetic Trees
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a026252openalex-snapshot
Multiple Maxima of Likelihood in Phylogenetic Trees: An Analytic Approach
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a040126openalex-snapshot
A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates.
inferredcites →https://doi.org/10.1093/sysbio/44.1.17openalex-snapshot
Performance of Phylogenetic Methods in Simulation
inferredcites →https://doi.org/10.1109/csb.2002.1039325openalex-snapshot
AxML: a fast program for sequential and parallel phylogenetic tree calculations based on the maximum likelihood method
inferredcites →https://doi.org/10.1109/ipdps.2005.90openalex-snapshot
An Efficient Program for Phylogenetic Inference Using Simulated Annealing
inferredcites →https://doi.org/10.2307/2005713openalex-snapshot
Algorithms for Minimization Without Derivatives
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
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Taxonomic reassessment of Blanus strauchi (Bedriaga, 1884) (Squamata: Amphisbaenia: Blanidae), with the description of a new species from south-east Anatolia (Turkey)
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Molecular Phylogeny Reconstruction
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Phylogenetic Likelihood
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Molecular Phylogeny Reconstruction
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Phylogenetic Search Algorithms for Maximum Likelihood
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Ancestral Haloalkane Dehalogenases Show Robustness and Unique Substrate Specificity
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Parallel Evolution of Transcription Factors in Basal Metazoans
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Detection and Analysis of Non-retroviral RNA Virus-Like Elements in Plant, Fungal, and Insect Genomes
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Estimating Maximum Likelihood Phylogenies with PhyML
inferred← citeshttps://doi.org/10.1007/978-3-030-10837-3_2openalex-snapshot
Numerical Optimization Techniques in Maximum Likelihood Tree Inference
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An Enhanced Algorithm for Reconstructing a Phylogenetic Tree Based on the Tree Rearrangement and Maximum Likelihood Method
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Accuracy Guarantees for Phylogeny Reconstruction Algorithms Based on Balanced Minimum Evolution
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Phylogeny of Animals: Genomes Have a Lot to Say
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Using Confidence Set Heuristics During Topology Search Improves the Robustness of Phylogenetic Inference
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Streptococcus nasisuis sp. nov., Isolated from a Pig with Respiratory Illness
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Anaerotalea alkaliphila gen. nov., sp. nov., an alkaliphilic, anaerobic, fermentative bacterium isolated from a terrestrial mud volcano
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Tentacle Transcriptomes of the Speckled Anemone (Actiniaria: Actiniidae: Oulactis sp.): Venom-Related Components and Their Domain Structure
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Effects of long-term discharge of acid mine drainage from abandoned coal mines on soil microorganisms: microbial community structure, interaction patterns, and metabolic functions
inferred← citeshttps://doi.org/10.1007/s11356-023-27403-5openalex-snapshot
Hydrochemical characteristics and microbial community evolution of Pinglu River affected by regional abandoned coal mine drainage, Guizhou Province, China
inferred← citeshttps://doi.org/10.1016/b978-0-323-95502-7.00255-4openalex-snapshot
Evolution of Genes and Proteins, and Their Gain or Loss of Function
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Maximum Likelihood Phylogenetic Inference
inferred← citeshttps://doi.org/10.1016/j.cub.2020.09.080openalex-snapshot
A Synthetic Approach to Reconstruct the Evolutionary and Functional Innovations of the Plant Histone Variant H2A.W
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Heterogeneity in the genus Allovahlkampfia and the description of the new genus Parafumarolamoeba (Vahlkampfiidae; Heterolobosea)
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Markov invariants, plethysms, and phylogenetics
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Using phylogeography to characterize the origins of the HIV-1 subtype F epidemic in Romania
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Molecular data confirm family status for the Tryonicus–Lauraesilpha group (Insecta: Blattodea: Tryonicidae)
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Characterization of a Vitis vinifera cv. Cabernet Sauvignon 3′,5′-O-methyltransferase showing strong preference for anthocyanins and glycosylated flavonols
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Koleobacter methoxysyntrophicus gen. nov., sp. nov., a novel anaerobic bacterium isolated from deep subsurface oil field and proposal of Koleobacteraceae fam. nov. and Koleobacterales ord. nov. within the class Clostridia of the phylum Firmicutes
inferred← citeshttps://doi.org/10.1016/j.syapm.2022.126356openalex-snapshot
Natranaeroarchaeum sulfidigenes gen. nov., sp. nov., carbohydrate-utilizing sulfur-respiring haloarchaeon from hypersaline soda lakes, a member of a new family Natronoarchaeaceae fam. nov. in the order Halobacteriales
inferred← citeshttps://doi.org/10.1016/j.toxicon.2011.12.014openalex-snapshot
Convergent evolution led ribosome inactivating proteins to interact with ribosomal stalk
inferred← citeshttps://doi.org/10.1016/j.vetmic.2010.06.030openalex-snapshot
Direct typing and molecular evolutionary analysis of field samples of foot-and-mouth disease virus collected in Viet Nam between 2006 and 2007
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A novel quadripartite dsRNA virus isolated from a phytopathogenic filamentous fungus, Rosellinia necatrix
inferred← citeshttps://doi.org/10.1016/j.virol.2012.10.002openalex-snapshot
Evidence for negative-strand RNA virus infection in fungi
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Origin of Pax and Six gene families in sponges: Single PaxB and Six1/2 orthologs in Chalinula loosanoffi
inferred← citeshttps://doi.org/10.1016/j.ympev.2010.01.007openalex-snapshot
Slow worm, Anguis fragilis (Reptilia: Anguidae) as a species complex: Genetic structure reveals deep divergences
inferred← citeshttps://doi.org/10.1016/j.ympev.2010.03.015openalex-snapshot
Phylogeography of the Middle Eastern tree frogs (Hyla, Hylidae, Amphibia) as inferred from nuclear and mitochondrial DNA variation, with a description of a new species
inferred← citeshttps://doi.org/10.1016/j.ympev.2011.08.029openalex-snapshot
morePhyML: Improving the phylogenetic tree space exploration with PhyML 3
inferred← citeshttps://doi.org/10.1016/j.ympev.2011.11.030openalex-snapshot
Opsin gene duplication and divergence in ray-finned fish
inferred← citeshttps://doi.org/10.1016/s0065-2458(06)68004-2openalex-snapshot
Computational Grand Challenges in Assembling the Tree of Life: Problems and Solutions
inferred← citeshttps://doi.org/10.1017/s003118201000096xopenalex-snapshot
cAMP-dependent protein kinase fromPlasmodium falciparum: an update
inferred← citeshttps://doi.org/10.1021/acscatal.9b01031openalex-snapshot
Light-Emitting Dehalogenases: Reconstruction of Multifunctional Biocatalysts
inferred← citeshttps://doi.org/10.1021/bi100009popenalex-snapshot
Stimulation of Lignocellulosic Biomass Hydrolysis by Proteins of Glycoside Hydrolase Family 61: Structure and Function of a Large, Enigmatic Family
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Analyzing the Hydrophobic Proteome of the Antarctic Archaeon Methanococcoides burtonii Using Differential Solubility Fractionation
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The evolutionary landscape of intergenic trans-splicing events in insects
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Harnessing machine learning to guide phylogenetic-tree search algorithms
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Metagenomic-based Surveillance of Pacific Coast tick Dermacentor occidentalis Identifies Two Novel Bunyaviruses and an Emerging Human Ricksettsial Pathogen
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Xrp1 is a transcription factor required for cell competition-driven elimination of loser cells
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A novel endogenous selection marker for the diatom Phaeodactylum tricornutum based on a unique mutation in phytoene desaturase 1
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Transmission dynamics of HIV-1 subtype B strains in Indonesia
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Genomics, biogeography, and the diversification of placental mammals
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Combinatorics of distance-based tree inference
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Deciphering the evolution of flavin-dependent monooxygenase stereoselectivity using ancestral sequence reconstruction
inferred← citeshttps://doi.org/10.1080/10635150701779808openalex-snapshot
Increasing the Efficiency of Searches for the Maximum Likelihood Tree in a Phylogenetic Analysis of up to 150 Nucleotide Sequences
inferred← citeshttps://doi.org/10.1080/10635150802429642openalex-snapshot
A Rapid Bootstrap Algorithm for the RAxML Web Servers
inferred← citeshttps://doi.org/10.1080/19336934.2015.1101196openalex-snapshot
The aminoacyl-tRNA synthetases ofDrosophila melanogaster
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The Rab7 subfamily across Paramecium aurelia species; evidence of high conservation in sequence and function
inferred← citeshttps://doi.org/10.1089/aid.2019.0150openalex-snapshot
Recombination Analysis of Near Full-Length HIV-1 Sequences and the Identification of a Potential New Circulating Recombinant Form from Rakai, Uganda
inferred← citeshttps://doi.org/10.1089/cmb.2015.0146openalex-snapshot
Consequences of Common Topological Rearrangements for Partition Trees in Phylogenomic Inference
inferred← citeshttps://doi.org/10.1091/mbc.e16-06-0361openalex-snapshot
Early stages of functional diversification in the Rab GTPase gene family revealed by genomic and localization studies inParameciumspecies
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199549429.001.0001openalex-snapshot
Animal Evolution
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199549429.002.0003openalex-snapshot
Copyright Page
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199549429.002.0007openalex-snapshot
Contributors
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199549429.002.0008openalex-snapshot
Introduction
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199549429.003.0001openalex-snapshot
The earliest fossil record of the animals and its significance
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199549429.003.0002openalex-snapshot
The Ediacaran emergence of bilaterians: congruence between the genetic and the geological fossil records
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199549429.003.0003openalex-snapshot
Genomic, phylogenetic, and cell biological insights into metazoan origins
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199549429.003.0004openalex-snapshot
The mouth, the anus, and the blastopore—open questions about questionable openings
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199549429.003.0005openalex-snapshot
Origins of metazoan body plans: the larval revolution
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199549429.003.0006openalex-snapshot
Assembling the spiralian tree of life
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199549429.003.0007openalex-snapshot
The evolution of nervous system centralization
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199549429.003.0008openalex-snapshot
The origins and evolution of the Ecdysozoa
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199549429.003.0009openalex-snapshot
Deciphering deuterostome phylogeny: molecular, morphological, and palaeontological perspectives
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199549429.003.0010openalex-snapshot
Molecular genetic insights into deuterostome evolution from the direct-developing hemichordateSaccoglossus kowalevskii
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199549429.003.0011openalex-snapshot
Invertebrate Problematica: kinds, causes, and solutions
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199549429.003.0012openalex-snapshot
Improvement of molecular phylogenetic inference and the phylogeny of Bilateria
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199549429.003.0013openalex-snapshot
Beyond linear sequence comparisons: the use of genome-level characters for phylogenetic reconstruction
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199549429.003.0014openalex-snapshot
The animal in the genome: comparative genomics and evolution
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199549429.003.0015openalex-snapshot
MicroRNAs and metazoan phylogeny: big trees from little genes
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199549429.003.0016openalex-snapshot
The evolution of developmental gene networks: lessons from comparative studies on holometabolous insects
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199549429.003.0017openalex-snapshot
Conserved developmental processes and the evolution of novel traits: wounds, embryos, veins, and butterfly eyespots
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199549429.003.0018openalex-snapshot
Reassembling animal evolution: a four-dimensional puzzle
inferred← citeshttps://doi.org/10.1093/bib/bbaf732openalex-snapshot
Learning to explore tree neighbourhoods for phylogenetic inference
inferred← citeshttps://doi.org/10.1093/bioinformatics/btac252openalex-snapshot
A LASSO-based approach to sample sites for phylogenetic tree search
inferred← citeshttps://doi.org/10.1093/bioinformatics/btad660openalex-snapshot
An evolution strategy approach for the balanced minimum evolution problem
inferred← citeshttps://doi.org/10.1093/bioinformatics/btl446openalex-snapshot
RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
inferred← citeshttps://doi.org/10.1093/bioinformatics/btn445openalex-snapshot
Empirical profile mixture models for phylogenetic reconstruction
inferred← citeshttps://doi.org/10.1093/bioinformatics/btw632openalex-snapshot
State aggregation for fast likelihood computations in molecular evolution
inferred← citeshttps://doi.org/10.1093/g3journal/jkae060openalex-snapshot
Identification of chemosensory genes in the stingless bee Tetragonisca fiebrigi
inferred← citeshttps://doi.org/10.1093/gbe/evab185openalex-snapshot
Evolution of the Insect PPK Gene Family
inferred← citeshttps://doi.org/10.1093/gbe/evt056openalex-snapshot
An Advanced System of the Mitochondrial Processing Peptidase and Core Protein Family in Trypanosoma brucei and Multiple Origins of the Core I Subunit in Eukaryotes
inferred← citeshttps://doi.org/10.1093/molbev/msl039openalex-snapshot
Testing the Molecular Clock: Molecular and Paleontological Estimates of Divergence Times in the Echinoidea (Echinodermata)
inferred← citeshttps://doi.org/10.1093/molbev/msl137openalex-snapshot
Lack of Resolution in the Animal Phylogeny: Closely Spaced Cladogeneses or Undetected Systematic Errors?
inferred← citeshttps://doi.org/10.1093/molbev/msn067openalex-snapshot
An Improved General Amino Acid Replacement Matrix
inferred← citeshttps://doi.org/10.1093/molbev/msq059openalex-snapshot
Phylogenomic Evidence for Separate Acquisition of Plastids in Cryptophytes, Haptophytes, and Stramenopiles
inferred← citeshttps://doi.org/10.1093/molbev/mst034openalex-snapshot
CodonPhyML: Fast Maximum Likelihood Phylogeny Estimation under Codon Substitution Models
inferred← citeshttps://doi.org/10.1093/molbev/msu300openalex-snapshot
IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies
inferred← citeshttps://doi.org/10.1093/sysbio/syaa068openalex-snapshot
An Evolving View of Phylogenetic Support
inferred← citeshttps://doi.org/10.1093/sysbio/syq002openalex-snapshot
Accounting for Solvent Accessibility and Secondary Structure in Protein Phylogenetics Is Clearly Beneficial
inferred← citeshttps://doi.org/10.1093/sysbio/syq010openalex-snapshot
New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0
inferred← citeshttps://doi.org/10.1093/sysbio/syr021openalex-snapshot
Bayes Estimators for Phylogenetic Reconstruction
inferred← citeshttps://doi.org/10.1093/sysbio/syr041openalex-snapshot
Survey of Branch Support Methods Demonstrates Accuracy, Power, and Robustness of Fast Likelihood-based Approximation Schemes
inferred← citeshttps://doi.org/10.1093/sysbio/syt022openalex-snapshot
PhyloBayes MPI: Phylogenetic Reconstruction with Infinite Mixtures of Profiles in a Parallel Environment
inferred← citeshttps://doi.org/10.1093/sysbio/syu048openalex-snapshot
The Inference of Gene Trees with Species Trees
inferred← citeshttps://doi.org/10.1097/qad.0000000000001763openalex-snapshot
Increase in transmitted drug resistance in migrants from sub-Saharan Africa diagnosed with HIV-1 in Sweden
inferred← citeshttps://doi.org/10.1098/rspb.2014.0848openalex-snapshot
Frequent, independent transfers of a catabolic gene from bacteria to contrasted filamentous eukaryotes
inferred← citeshttps://doi.org/10.1098/rstb.2007.2236openalex-snapshot
Improvement of molecular phylogenetic inference and the phylogeny of Bilateria
inferred← citeshttps://doi.org/10.1098/rstb.2008.0180openalex-snapshot
Phylogenetic mixture models for proteins
inferred← citeshttps://doi.org/10.1099/ijsem.0.002810openalex-snapshot
Methanonatronarchaeum thermophilum gen. nov., sp. nov. and 'Candidatus Methanohalarchaeum thermophilum', extremely halo(natrono)philic methyl-reducing methanogens from hypersaline lakes comprising a new euryarchaeal class Methanonatronarchaeia classis nov.
inferred← citeshttps://doi.org/10.1099/ijsem.0.004019openalex-snapshot
Calorimonas adulescens gen. nov., sp. nov., an anaerobic thermophilic bacterium utilizing methoxylated benzoates
inferred← citeshttps://doi.org/10.1099/ijsem.0.004361openalex-snapshot
Alkalibaculum sporogenes sp. nov., isolated from a terrestrial mud volcano and emended description of the genus Alkalibaculum
inferred← citeshttps://doi.org/10.1099/ijsem.0.005174openalex-snapshot
Alkalibacter mobilis sp. nov., an anaerobic bacterium isolated from a coastal lake
inferred← citeshttps://doi.org/10.1099/jgv.0.000878openalex-snapshot
Hepatitis C virus subtype 3a was introduced in the USSR in the early 1980s
inferred← citeshttps://doi.org/10.1099/mgen.0.000156openalex-snapshot
Assembly of highly repetitive genomes using short reads: the genome of discrete typing unit III Trypanosoma cruzi strain 231
inferred← citeshttps://doi.org/10.1099/mic.0.000668openalex-snapshot
Linkage of the Nit1C gene cluster to bacterial cyanide assimilation as a nitrogen source
inferred← citeshttps://doi.org/10.1101/035063openalex-snapshot
State aggregation for fast likelihood computations in molecular evolution
inferred← citeshttps://doi.org/10.1101/2020.11.05.369660openalex-snapshot
The FUR-like regulators PerRA and PerRB integrate a complex regulatory network that promotes mammalian host-adaptation and virulence of Leptospira interrogans
inferred← citeshttps://doi.org/10.1101/2024.11.08.622704openalex-snapshot
Large-scale Inference of Cell Lineage Trees and Genotype Calling from Noisy Single-Cell Data Using Efficient Local Search
inferred← citeshttps://doi.org/10.1101/467894openalex-snapshot
Ribosomal protein imbalance launches a C/EBP-based program to preserve tissue integrity
inferred← citeshttps://doi.org/10.1101/671420openalex-snapshot
Exploring novel probiotic mechanisms of Streptococcus A12 with functional genomics
inferred← citeshttps://doi.org/10.1101/gr.280542.125openalex-snapshot
ScisTree2 enables large-scale inference of cell lineage trees and genotype calling using efficient local search
inferred← citeshttps://doi.org/10.1109/access.2020.3043150openalex-snapshot
Deep Neighbor Information Learning From Evolution Trees for Phylogenetic Likelihood Estimates
inferred← citeshttps://doi.org/10.1109/icpp.2009.29openalex-snapshot
Load Balance in the Phylogenetic Likelihood Kernel
inferred← citeshttps://doi.org/10.1109/imsccs.2007.49openalex-snapshot
Varying the Sample Number for Monte Carlo Localization in Mobile Sensor Networks
inferred← citeshttps://doi.org/10.1109/imsccs.2007.90openalex-snapshot
Improving the Efficiency of p-ECR Moves in Evolutionary TreeSearch Methods Based on Maximum Likelihood by Neighbor Joining
inferred← citeshttps://doi.org/10.1109/tcbb.2008.37openalex-snapshot
Consistency of Topological Moves Based on the Balanced Minimum Evolution Principle of Phylogenetic Inference
inferred← citeshttps://doi.org/10.1109/tcbb.2013.39openalex-snapshot
Accuracy Guarantees for Phylogeny Reconstruction Algorithms Based on Balanced Minimum Evolution
inferred← citeshttps://doi.org/10.1111/1574-6968.12548openalex-snapshot
Expansion of ability of denitrification within the filamentous colorless sulfur bacteria of the genusThiothrix
inferred← citeshttps://doi.org/10.1111/ibi.12683openalex-snapshot
Multi‐locus phylogeny of African pipits and longclaws (Aves: Motacillidae) highlights taxonomic inconsistencies
inferred← citeshttps://doi.org/10.1111/j.1550-7408.2009.00430.xopenalex-snapshot
Description and Phylogenetic Relationships of Spumochlamys perforata n. sp. and Spumochlamys bryora n. sp. (Amoebozoa, Arcellinida)
inferred← citeshttps://doi.org/10.1111/jbi.12057openalex-snapshot
Comparative phylogeography reveals distinct colonization patterns of C retan snakes
inferred← citeshttps://doi.org/10.1111/nph.14590openalex-snapshot
Arabidopsis thaliana EPOXIDE HYDROLASE1 (AtEH1) is a cytosolic epoxide hydrolase involved in the synthesis of poly‐hydroxylated cutin monomers
inferred← citeshttps://doi.org/10.1126/science.aac5017openalex-snapshot
Dengue viruses cluster antigenically but not as discrete serotypes
inferred← citeshttps://doi.org/10.1128/aem.01335-19openalex-snapshot
Novel Probiotic Mechanisms of the Oral Bacterium Streptococcus sp. A12 as Explored with Functional Genomics
inferred← citeshttps://doi.org/10.1128/aem.02636-10openalex-snapshot
Investigation of Genotypes of Borrelia burgdorferi in Ixodes scapularis Ticks Collected during Surveillance in Canada
inferred← citeshttps://doi.org/10.1128/aem.05909-11openalex-snapshot
Intergenic Sequence Comparison of Escherichia coli Isolates Reveals Lifestyle Adaptations but Not Host Specificity
inferred← citeshttps://doi.org/10.1128/jb.00436-15openalex-snapshot
Cross Talk Inhibition Nullified by a Receiver Domain Missense Substitution
inferred← citeshttps://doi.org/10.1128/jvi.00557-13openalex-snapshot
A Novel Victorivirus from a Phytopathogenic Fungus, Rosellinia necatrix, Is Infectious as Particles and Targeted by RNA Silencing
inferred← citeshttps://doi.org/10.1128/jvi.00828-11openalex-snapshot
Widespread Endogenization of Densoviruses and Parvoviruses in Animal and Human Genomes
inferred← citeshttps://doi.org/10.1128/jvi.00955-10openalex-snapshot
Widespread Horizontal Gene Transfer from Double-Stranded RNA Viruses to Eukaryotic Nuclear Genomes
inferred← citeshttps://doi.org/10.1128/jvi.02835-12openalex-snapshot
Effects of Defective Interfering RNA on Symptom Induction by, and Replication of, a Novel Partitivirus from a Phytopathogenic Fungus, Rosellinia necatrix
inferred← citeshttps://doi.org/10.1128/mcb.00799-10openalex-snapshot
Basic Leucine Zipper Protein Cnc-C Is a Substrate and Transcriptional Regulator of the Drosophila 26S Proteasome
inferred← citeshttps://doi.org/10.1128/spectrum.00725-22openalex-snapshot
Evolution of Multiple Domains of the HIV-1 Envelope Glycoprotein during Coreceptor Switch with CCR5 Antagonist Therapy
inferred← citeshttps://doi.org/10.1145/3316615.3316630openalex-snapshot
GPU Accelerated Maximum Likelihood Analysis for Phylogenetic Inference
inferred← citeshttps://doi.org/10.1145/3747592openalex-snapshot
Accelerated Phylogenetics on the AMD Versal Adaptive SoC
inferred← citeshttps://doi.org/10.1163/15685381-00002927openalex-snapshot
Distribution and hybridization of Anguis fragilis and A. colchica in Hungary
inferred← citeshttps://doi.org/10.1177/117693430700300014openalex-snapshot
Efficient Tree Searches with Available Algorithms
inferred← citeshttps://doi.org/10.1186/1471-2105-9-s6-s4openalex-snapshot
A topological transformation in evolutionary tree search methods based on maximum likelihood combining p-ECR and neighbor joining
inferred← citeshttps://doi.org/10.1186/1471-2148-11-276openalex-snapshot
Widespread Horizontal Gene Transfer from Circular Single-stranded DNA Viruses to Eukaryotic Genomes
inferred← citeshttps://doi.org/10.1186/1471-2148-12-140openalex-snapshot
The mammalian PYHIN gene family: Phylogeny, evolution and expression
inferred← citeshttps://doi.org/10.1186/1471-2148-12-148openalex-snapshot
Multiple functionally divergent and conserved copies of alpha tubulin in bdelloid rotifers
inferred← citeshttps://doi.org/10.1186/1471-2164-13-75openalex-snapshot
Identification and localisation of the NB-LRR gene family within the potato genome
inferred← citeshttps://doi.org/10.1186/1743-422x-8-310openalex-snapshot
Novel norovirus recombinants and GII.4 sub-lineages associated with outbreaks between 2006 and 2010 in Belgium
inferred← citeshttps://doi.org/10.1186/s12864-015-2090-3openalex-snapshot
First complete mitochondrial genome of the South American annual fish Austrolebias charrua (Cyprinodontiformes: Rivulidae): peculiar features among cyprinodontiforms mitogenomes
inferred← citeshttps://doi.org/10.1186/s12864-022-08974-yopenalex-snapshot
Comparative analysis of detoxification-related gene superfamilies across five hemipteran species
inferred← citeshttps://doi.org/10.1186/s12864-022-09059-6openalex-snapshot
The antennal transcriptome of Triatoma infestans reveals substantial expression changes triggered by a blood meal
inferred← citeshttps://doi.org/10.1186/s13059-018-1606-yopenalex-snapshot
Recombination of ecologically and evolutionarily significant loci maintains genetic cohesion in the Pseudomonas syringae species complex
inferred← citeshttps://doi.org/10.1186/s13071-019-3461-4openalex-snapshot
Zika virus detection, isolation and genome sequencing through Culicidae sampling during the epidemic in Vitória, Espírito Santo, Brazil
inferred← citeshttps://doi.org/10.12794/metadc1505253openalex-snapshot
Defining Components Linked to Bacterial Nutritional Utilization of Cyanide as a Sole Nitrogen Source
inferred← citeshttps://doi.org/10.1371/journal.pgen.0030002openalex-snapshot
Early History of Mammals Is Elucidated with the ENCODE Multiple Species Sequencing Data
inferred← citeshttps://doi.org/10.1371/journal.pgen.1008964openalex-snapshot
The evolution and functional divergence of the histone H2B family in plants
inferred← citeshttps://doi.org/10.1371/journal.pone.0002651openalex-snapshot
Phylogenetic Detection of Recombination with a Bayesian Prior on the Distance between Trees
inferred← citeshttps://doi.org/10.1371/journal.pone.0009490openalex-snapshot
FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments
inferred← citeshttps://doi.org/10.1371/journal.pone.0064270openalex-snapshot
Evolution of and Horizontal Gene Transfer in the Endornavirus Genus
inferred← citeshttps://doi.org/10.1371/journal.pone.0094162openalex-snapshot
Geographic Variation of Melanisation Patterns in a Hornet Species: Genetic Differences, Climatic Pressures or Aposematic Constraints?
inferred← citeshttps://doi.org/10.1371/journal.ppat.1002146openalex-snapshot
Widespread Endogenization of Genome Sequences of Non-Retroviral RNA Viruses into Plant Genomes
inferred← citeshttps://doi.org/10.1371/journal.ppat.1009078openalex-snapshot
The FUR-like regulators PerRA and PerRB integrate a complex regulatory network that promotes mammalian host-adaptation and virulence of Leptospira interrogans
inferred← citeshttps://doi.org/10.14445/22315381/ijett-v65p204openalex-snapshot
Well- Established Bootstrap Algorithms
inferred← citeshttps://doi.org/10.20868/upm.thesis.14937openalex-snapshot
Coevolución virus-planta: impacto de las infecciones virales en poblaciones silvestres de Chiltepín (capsicum annuum var. Aviculare (dierbach) d’arcy & eshbaugh) en México.
inferred← citeshttps://doi.org/10.2478/10004-1254-65-2014-2421openalex-snapshot
First evidence of the P-glycoprotein gene expression and multixenobiotic resistance modulation in earthworm
inferred← citeshttps://doi.org/10.3161/150811010x504617openalex-snapshot
Taxonomy of the GenusOtonycteris(Chiroptera: Vespertilionidae: Plecotini) as Inferred from Morphological and mtDNA Data
inferred← citeshttps://doi.org/10.3389/fcell.2023.1113046openalex-snapshot
Transposon-derived transcription factors across metazoans
inferred← citeshttps://doi.org/10.3389/fgene.2022.997341openalex-snapshot
Investigating CRISPR spacer targets and their impact on genomic diversification of Streptococcus mutans
inferred← citeshttps://doi.org/10.3389/fimmu.2018.00304openalex-snapshot
Coevolution of the Toll-Like Receptor 4 Complex with Calgranulins and Lipopolysaccharide
inferred← citeshttps://doi.org/10.3389/fmicb.2015.01504openalex-snapshot
The Microbial Opsin Homolog Sop1 is involved in Sclerotinia sclerotiorum Development and Environmental Stress Response
inferred← citeshttps://doi.org/10.3389/fmicb.2022.797463openalex-snapshot
A Comprehensive Analysis of Citrus Tristeza Variants of Bhutan and Across the World
inferred← citeshttps://doi.org/10.3390/d14020108openalex-snapshot
Strong Philopatry, Isolation by Distance, and Local Habitat Have Promoted Genetic Structure in Heermann’s Gull
inferred← citeshttps://doi.org/10.3390/genes13050917openalex-snapshot
Characterization, Selection, and Trans-Species Polymorphism in the MHC Class II of Heermann’s Gull (Charadriiformes)
inferred← citeshttps://doi.org/10.3390/ijms17040599openalex-snapshot
In Silico Structure and Sequence Analysis of Bacterial Porins and Specific Diffusion Channels for Hydrophilic Molecules: Conservation, Multimericity and Multifunctionality
inferred← citeshttps://doi.org/10.3390/microorganisms8101532openalex-snapshot
Combined Use of Diagnostic Fumarate Addition Metabolites and Genes Provides Evidence for Anaerobic Hydrocarbon Biodegradation in Contaminated Groundwater
inferred← citeshttps://doi.org/10.3390/pathogens13111001openalex-snapshot
The Evolution of Wisteria Vein Mosaic Virus: A Case Study Approach to Track the Emergence of New Potyvirus Threats
inferred← citeshttps://doi.org/10.3390/v12111301openalex-snapshot
Identification of Novel Astroviruses in the Gastrointestinal Tract of Domestic Cats
inferred← citeshttps://doi.org/10.3390/v17050734openalex-snapshot
Phylogenetic Analysis and Spread of HPAI H5N1 in Middle Eastern Countries Based on Hemagglutinin and Neuraminidase Gene Sequences
inferred← citeshttps://doi.org/10.3724/sp.j.1002.2008.08038openalex-snapshot
Animal phylogeny and large-scale sequencing: progress and pitfalls
inferred← citeshttps://doi.org/10.4049/jimmunol.1901288openalex-snapshot
Identification and Characterization of Zebrafish Tlr4 Coreceptor Md-2
inferred← citeshttps://doi.org/10.4137/ebo.s4528openalex-snapshot
Maximum Likelihood Analyses of 3,490 rbcL Sequences: Scalability of Comprehensive Inference versus Group-Specific Taxon Sampling
inferred← citeshttps://doi.org/10.4172/2329-9002openalex-snapshot
Journal of Phylogenetics & Evolutionary Biology
inferred← citeshttps://doi.org/10.4269/ajtmh.2010.10-0023openalex-snapshot
Index Cluster Study of Dengue Virus Infection in Nicaragua
inferred← citeshttps://doi.org/10.48550/arxiv.0711.3503openalex-snapshot
Markov invariants, plethysms, and phylogenetics (the long version)
inferred← citeshttps://doi.org/10.48550/arxiv.0912.5288openalex-snapshot
Resampling Residuals: Robust Estimators of Error and Fit for Evolutionary Trees and Phylogenomics
inferred← citeshttps://doi.org/10.48550/arxiv.1012.5882openalex-snapshot
What use are Exponential Weights for flexi-Weighted Least Squares Phylogenetic Trees?
inferred← citeshttps://doi.org/10.48550/arxiv.1012.5887openalex-snapshot
A Unified Framework for Trees, Multi-Dimensional Scaling and Planar Graphs
inferred← citeshttps://doi.org/10.48550/arxiv.1101.0020openalex-snapshot
Resampling Residuals on Phylogenetic Trees: Extended Results
inferred← citeshttps://doi.org/10.48550/arxiv.1407.7619openalex-snapshot
A Statistical Test for Clades in Phylogenies
inferred← citeshttps://doi.org/10.5772/48336openalex-snapshot
Ribosomes from Trypanosomatids: Unique Structural and Functional Properties
inferred← citeshttps://doi.org/10.64898/2025.12.19.695395openalex-snapshot
Structural network comparison of domains across remote homologues arising from different domain architectures
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