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Evaluating Fast Maximum Likelihood-Based Phylogenetic Programs Using Empirical Phylogenomic Data Sets
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
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Using RAxML to Infer Phylogenies
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Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods
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Evolutionary trees from DNA sequences: A maximum likelihood approach
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Exploring New Search Algorithms and Hardware for Phylogenetics: RAxML Meets the IBM Cell
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Comparison of phylogenetic trees
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Comparison of labeled trees with valency three
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The Evolution of Annelids Reveals Two Adaptive Routes to the Interstitial Realm
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Genome-scale approaches to resolving incongruence in molecular phylogenies
inferredcites →https://doi.org/10.1038/nature15697openalex-snapshot
A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing
inferredcites →https://doi.org/10.1038/nature19417openalex-snapshot
A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing
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Latent homology and convergent regulatory evolution underlies the repeated emergence of yeasts
inferredcites →https://doi.org/10.1038/nmicrobiol.2016.48openalex-snapshot
A new view of the tree of life
inferredcites →https://doi.org/10.1038/nrg3186openalex-snapshot
Molecular phylogenetics: principles and practice
inferredcites →https://doi.org/10.1038/s41559-017-0126openalex-snapshot
Contentious relationships in phylogenomic studies can be driven by a handful of genes
inferredcites →https://doi.org/10.1073/pnas.1211733109openalex-snapshot
Resolving conflict in eutherian mammal phylogeny using phylogenomics and the multispecies coalescent model
inferredcites →https://doi.org/10.1073/pnas.1323926111openalex-snapshot
Phylotranscriptomic analysis of the origin and early diversification of land plants
inferredcites →https://doi.org/10.1073/pnas.1503453112openalex-snapshot
Error, signal, and the placement of Ctenophora sister to all other animals
inferredcites →https://doi.org/10.1080/10635150290069913openalex-snapshot
An Approximately Unbiased Test of Phylogenetic Tree Selection
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A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood
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Molecular Evolution
inferredcites →https://doi.org/10.1093/bioinformatics/bti191openalex-snapshot
RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees
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RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
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RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
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ExaML version 3: a tool for phylogenomic analyses on supercomputers
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ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes
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The Interrelationships of Placental Mammals and the Limits of Phylogenetic Inference
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A Genome-Scale Investigation of How Sequence, Function, and Tree-Based Gene Properties Influence Phylogenetic Inference
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IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies
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Dissecting Molecular Evolution in the Highly Diverse Plant Clade Caryophyllales Using Transcriptome Sequencing
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Fast Coalescent-Based Computation of Local Branch Support from Quartet Frequencies
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Mathematics of Evolution and Phylogeny
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Likelihood Calculation in Molecular Phylogenetics
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BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data
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Weighted Neighbor Joining: A Likelihood-Based Approach to Distance-Based Phylogeny Reconstruction
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The neighbor-joining method: a new method for reconstructing phylogenetic trees.
inferredcites →https://doi.org/10.1093/sysbio/syq010openalex-snapshot
New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0
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Characterizing the Phylogenetic Tree-Search Problem
inferredcites →https://doi.org/10.1093/sysbio/syu055openalex-snapshot
Coalescent versus Concatenation Methods and the Placement of Amborella as Sister to Water Lilies
inferredcites →https://doi.org/10.1093/sysbio/syu084openalex-snapshot
The Phylogenetic Likelihood Library
inferredcites →https://doi.org/10.1093/sysbio/syu126openalex-snapshot
Taxon-Rich Phylogenomic Analyses Resolve the Eukaryotic Tree of Life and Reveal the Power of Subsampling by Sites
inferredcites →https://doi.org/10.1093/sysbio/syv055openalex-snapshot
Automation and Evaluation of the SOWH Test with SOWHAT
inferredcites →https://doi.org/10.1093/sysbio/syv059openalex-snapshot
Selecting Question-Specific Genes to Reduce Incongruence in Phylogenomics: A Case Study of Jawed Vertebrate Backbone Phylogeny
inferredcites →https://doi.org/10.1093/sysbio/syw037openalex-snapshot
Terrace Aware Data Structure for Phylogenomic Inference from Supermatrices
inferredcites →https://doi.org/10.1109/gce18454.2010openalex-snapshot
2010 Gateway Computing Environments Workshop (GCE)
inferredcites →https://doi.org/10.1111/nyas.12747openalex-snapshot
Estimating phylogenetic trees from genome‐scale data
inferredcites →https://doi.org/10.1126/science.1250463openalex-snapshot
Statistical binning enables an accurate coalescent-based estimation of the avian tree
inferredcites →https://doi.org/10.1126/science.1253451openalex-snapshot
Whole-genome analyses resolve early branches in the tree of life of modern birds
inferredcites →https://doi.org/10.1126/science.1257570openalex-snapshot
Phylogenomics resolves the timing and pattern of insect evolution
inferredcites →https://doi.org/10.1186/s12864-015-2146-4openalex-snapshot
Extracting phylogenetic signal and accounting for bias in whole-genome data sets supports the Ctenophora as sister to remaining Metazoa
inferredcites →https://doi.org/10.1371/journal.pone.0009490openalex-snapshot
FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments
inferredcites →https://doi.org/10.1371/journal.pone.0027731openalex-snapshot
RAxML and FastTree: Comparing Two Methods for Large-Scale Maximum Likelihood Phylogeny Estimation
inferredcites →https://doi.org/10.1525/california/9780520276581.001.0001openalex-snapshot
Evolution of Phylogenetic Systematics
inferredcites →https://doi.org/10.1534/g3.116.034744openalex-snapshot
Reconstructing the Backbone of the Saccharomycotina Yeast Phylogeny Using Genome-Scale Data
inferredcites →https://doi.org/10.5860/choice.52-0262openalex-snapshot
The Evolution of phylogenetic systematics
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Incoming claims: where this work appears in other papers’ reference lists and arguments.
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Quartet-Based Computations of Internode Certainty Provide Robust Measures of Phylogenetic Incongruence
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Horizontal gene flow into Geobacillus is constrained by the chromosomal organization of growth and sporulation
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RAxML-NG: A fast, scalable, and user-friendly tool for maximum likelihood phylogenetic inference
inferred← citeshttps://doi.org/10.1101/527796openalex-snapshot
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A consensus phylogenomic approach highlights paleopolyploid and rapid radiation in the history of Ericales
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A Faster Algorithm for Computing the Kernel of Maximum Agreement Subtrees
inferred← citeshttps://doi.org/10.1111/1755-0998.13096openalex-snapshot
PhyloSuite: An integrated and scalable desktop platform for streamlined molecular sequence data management and evolutionary phylogenetics studies
inferred← citeshttps://doi.org/10.1111/1755-0998.13407openalex-snapshot
Assessment of current taxonomic assignment strategies for metabarcoding eukaryotes
inferred← citeshttps://doi.org/10.1111/2041-210x.70419openalex-snapshot
HGTScanner : Detecting horizontal gene transfer at the fine scale using whole organelle genomes
inferred← citeshttps://doi.org/10.1111/eva.13735openalex-snapshot
Using de novo transcriptomes to decipher the relationships in cutthroat trout subspecies (Oncorhynchus clarkii)
inferred← citeshttps://doi.org/10.1111/jse.12692openalex-snapshot
Thistle be a mess: Untangling the taxonomy of Cirsium (Cardueae: Compositae) in North America
inferred← citeshttps://doi.org/10.1111/mec.16781openalex-snapshot
Whole‐genome resequencing reveals complex effects of geographical–palaeoclimatic interactions on diversification of moustache toads in East Asia
inferred← citeshttps://doi.org/10.1111/syen.70050openalex-snapshot
From figs to acorns: Early specialization and host shifts shaped the global radiation of Curculionini weevils (Coleoptera: Curculionidae)
inferred← citeshttps://doi.org/10.1111/zsc.12407openalex-snapshot
Phylogeny of the superfamily Gelechioidea (Lepidoptera: Obtectomera), with an exploratory application on geometric morphometrics
inferred← citeshttps://doi.org/10.1126/sciadv.abd0079openalex-snapshot
Genome-scale phylogeny and contrasting modes of genome evolution in the fungal phylum Ascomycota
inferred← citeshttps://doi.org/10.1128/mbio.00925-19openalex-snapshot
A Robust Phylogenomic Time Tree for Biotechnologically and Medically Important Fungi in the Genera Aspergillus and Penicillium
inferred← citeshttps://doi.org/10.1155/2024/7945955openalex-snapshot
Predicting Potential PRRSV‐2 Variant Emergence through Phylogenetic Inference
inferred← citeshttps://doi.org/10.11606/t.41.2018.tde-20082018-134133openalex-snapshot
Systematics and evolution of the orb-weaving spider genus Wagneriana F.O. Pickard-Cambridge, 1904 (Araneae; Araneidae)
inferred← citeshttps://doi.org/10.1186/s12859-019-3292-5openalex-snapshot
LMAP_S: Lightweight Multigene Alignment and Phylogeny eStimation
inferred← citeshttps://doi.org/10.1186/s12859-023-05527-2openalex-snapshot
EasyCGTree: a pipeline for prokaryotic phylogenomic analysis based on core gene sets
inferred← citeshttps://doi.org/10.1186/s12859-025-06034-2openalex-snapshot
CamITree: a streamlined software for phylogenetic analysis of viral and mitochondrial genomes
inferred← citeshttps://doi.org/10.1186/s13059-019-1832-yopenalex-snapshot
OrthoFinder: phylogenetic orthology inference for comparative genomics
inferred← citeshttps://doi.org/10.1186/s13059-021-02583-wopenalex-snapshot
CellPhy: accurate and fast probabilistic inference of single-cell phylogenies from scDNA-seq data
inferred← citeshttps://doi.org/10.1242/jcs.263466openalex-snapshot
An evolutionary perspective on the relationship between kinetochore size and CENP-E dependence for chromosome alignment
inferred← citeshttps://doi.org/10.12688/wellcomeopenres.14265.1openalex-snapshot
Evaluation of phylogenetic reconstruction methods using bacterial whole genomes: a simulation based study
inferred← citeshttps://doi.org/10.12688/wellcomeopenres.14265.2openalex-snapshot
Evaluation of phylogenetic reconstruction methods using bacterial whole genomes: a simulation based study
inferred← citeshttps://doi.org/10.1371/journal.pbio.3000255openalex-snapshot
Extensive loss of cell-cycle and DNA repair genes in an ancient lineage of bipolar budding yeasts
inferred← citeshttps://doi.org/10.1371/journal.pbio.3001827openalex-snapshot
OrthoSNAP: A tree splitting and pruning algorithm for retrieving single-copy orthologs from gene family trees
inferred← citeshttps://doi.org/10.1371/journal.pcbi.1009278openalex-snapshot
The evolutionary history of topological variations in the CPA/AT transporters
inferred← citeshttps://doi.org/10.1371/journal.pcbi.1010686openalex-snapshot
AvP: A software package for automatic phylogenetic detection of candidate horizontal gene transfers
inferred← citeshttps://doi.org/10.1371/journal.pone.0279597openalex-snapshot
Roadmap to the study of gene and protein phylogeny and evolution—A practical guide
inferred← citeshttps://doi.org/10.1371/journal.pone.0338039openalex-snapshot
Tunicates have a complex, highly dynamic TNF superfamily
inferred← citeshttps://doi.org/10.1645/24-138openalex-snapshot
Diversity, Host Range, and Specificity of Echinostomes (Family Echinostomatidae; Looss, 1899) in the Midwestern United States
inferred← citeshttps://doi.org/10.17348/jbrit.v15.i1.1064openalex-snapshot
Multiple complementary studies clarify which co-occurring congener presents the greatest hybridization threat to a rare Texas endemic wildflower (Hibiscus dasycalyx: Malvaceae)
inferred← citeshttps://doi.org/10.17537/2022.17.289openalex-snapshot
On Classification and Taxonomy of Coronaviruses (Riboviria, Nidovirales, Coronaviridae) with Special Focus on Severe Acute Respiratory Syndrome-Related Coronavirus 2 (SARS-CoV-2)
inferred← citeshttps://doi.org/10.25148/etd.fidc008966openalex-snapshot
Phylogenetic and Transcriptomic Analyses of Vision in Two Cave Adapted Crustaceans, Asellus aquaticus (Isopoda: Asellidae) and Niphargus hrabei (Amphipoda: Niphargidae).
inferred← citeshttps://doi.org/10.25148/etd.fidc009548openalex-snapshot
A Comparative Genomics Exploration of Inter-partner Metabolic Signaling in the Coral-algal Symbiosis
inferred← citeshttps://doi.org/10.33540/111openalex-snapshot
On uncovering and understanding interactions between bacteriophages and bacteria
inferred← citeshttps://doi.org/10.3389/fbinf.2022.871393openalex-snapshot
Metagenomic Analysis Using Phylogenetic Placement—A Review of the First Decade
inferred← citeshttps://doi.org/10.3389/fimmu.2021.642383openalex-snapshot
Schistosomiasis Drug Discovery in the Era of Automation and Artificial Intelligence
inferred← citeshttps://doi.org/10.3389/fmars.2024.1425922openalex-snapshot
Phylogenetic relationships and lineage-specific mitochondrial gene rearrangement in Ophiuroidea: insights from mitochondrial genomes
inferred← citeshttps://doi.org/10.3389/fmicb.2018.00771openalex-snapshot
GET_PHYLOMARKERS, a Software Package to Select Optimal Orthologous Clusters for Phylogenomics and Inferring Pan-Genome Phylogenies, Used for a Critical Geno-Taxonomic Revision of the Genus Stenotrophomonas
inferred← citeshttps://doi.org/10.3389/fmicb.2020.00843openalex-snapshot
Global Distribution and Evolution of Mycobacterium bovis Lineages
inferred← citeshttps://doi.org/10.3389/fpls.2020.00224openalex-snapshot
Transcriptional Regulation of Sorghum Stem Composition: Key Players Identified Through Co-expression Gene Network and Comparative Genomics Analyses
inferred← citeshttps://doi.org/10.3389/fpls.2022.909768openalex-snapshot
An open and continuously updated fern tree of life
inferred← citeshttps://doi.org/10.3389/fviro.2024.1433931openalex-snapshot
Phylogenetic-based methods for fine-scale classification of PRRSV-2 ORF5 sequences: a comparison of their robustness and reproducibility
inferred← citeshttps://doi.org/10.3390/a14050148openalex-snapshot
Disjoint Tree Mergers for Large-Scale Maximum Likelihood Tree Estimation
inferred← citeshttps://doi.org/10.3390/antibiotics10010074openalex-snapshot
Antimicrobial Resistance of Non-O157 Shiga Toxin-Producing Escherichia coli Isolated from Humans and Domestic Animals
inferred← citeshttps://doi.org/10.3390/biology14010054openalex-snapshot
Vertebrate TNF Superfamily: Evolution and Functional Insights
inferred← citeshttps://doi.org/10.3390/d15060705openalex-snapshot
Rediscovery of Five Rinodina Species Originally Described from Southwest China and One New Species
inferred← citeshttps://doi.org/10.3390/genes12010111openalex-snapshot
Defining the Rhizobium leguminosarum Species Complex
inferred← citeshttps://doi.org/10.3390/insects15020116openalex-snapshot
Fine-Scale Genetic Structure of Curculio chinensis (Coleoptera: Curculionidae) Based on Mitochondrial COI: The Role of Host Specificity and Spatial Distance
inferred← citeshttps://doi.org/10.3390/v11121085openalex-snapshot
Evolution of BACON Domain Tandem Repeats in crAssphage and Novel Gut Bacteriophage Lineages
inferred← citeshttps://doi.org/10.3390/v14040774openalex-snapshot
An Evaluation of Phylogenetic Workflows in Viral Molecular Epidemiology
inferred← citeshttps://doi.org/10.3410/f.734380463.793553343openalex-snapshot
Faculty Opinions recommendation of Tempo and mode of genome evolution in the budding yeast subphylum.
inferred← citeshttps://doi.org/10.3410/f.734380463.793554773openalex-snapshot
Faculty Opinions recommendation of Tempo and mode of genome evolution in the budding yeast subphylum.
inferred← citeshttps://doi.org/10.37828/em.2019.22.2openalex-snapshot
ESTIGENA WALLACEI SP. NOV. FROM WEST FLORES, INDONESIA (LEPIDOPTERA: LASIOCAMPIDAE)
inferred← citeshttps://doi.org/10.3897/zookeys.866.35084openalex-snapshot
Pollinators on the polar edge of the Ecumene: taxonomy, phylogeography, and ecology of bumble bees from Novaya Zemlya
inferred← citeshttps://doi.org/10.4049/jimmunol.1800498openalex-snapshot
Characterization of an NLRP1 Inflammasome from Zebrafish Reveals a Unique Sequential Activation Mechanism Underlying Inflammatory Caspases in Ancient Vertebrates
inferred← citeshttps://doi.org/10.53846/goediss-7229openalex-snapshot
Filtered spaced-word matches: a novel approach to fast and accurate sequence comparison
inferred← citeshttps://doi.org/10.5753/bsb_estendido.2018.8802openalex-snapshot
Avaliação do RAxML no Supercomputador Santos Dumont
inferred← citeshttps://doi.org/10.5943/cream/13/1/8openalex-snapshot
Characterization of White- and Brown-Rot Fungi Applied to the Decay of Caatinga Biome Wood (Swartzia psilonema Harms) from Brazil
inferred← citeshttps://doi.org/10.6084/m9.figshare.24311677openalex-snapshot
Additional file 1 of EasyCGTree: a pipeline for prokaryotic phylogenomic analysis based on core gene sets
inferred← citeshttps://doi.org/10.70675/471d1db2z2d6cz47e1z9450z321b9d09527copenalex-snapshot
Approche phylogénomique de la dynamique spatiale et temporelle de diversification chez les Lépidoptères Saturniidae
inferred← citeshttps://doi.org/10.70675/6f86394ezfb3az42e5z8e31z6d43f205fac3openalex-snapshot
Identification et validation de gènes pour l’amélioration du sorgho : de l’analyse transcriptomique à la validation fonctionnelle
inferred← citeshttps://doi.org/10.70675/a5e236dczd869z4c2aza5b7z105b4c6a4411openalex-snapshot
Evolution of protein motifs in their structural context : from mining motif resources available to the prediction of phenotype-specific motifs
inferred← citeshttps://doi.org/10.70675/ae8068bczf028z4169zbce3z1d87800eb1ccopenalex-snapshot
Évolution des gènes et génomes après duplication complète du génome chez les poissons téléostéens
inferred← citeshttps://doi.org/10.70675/af029f96z2aa2z437dzb6cezb2ecf72a3891openalex-snapshot
Apport des outils de biologie moléculaire dans l'étude et la surveillance du SARS-CoV-2 au cours de la pandémie de COVID-19
inferred← citeshttps://doi.org/10.7324/jabb.2024.163103openalex-snapshot
Refined Evolutionary Trees Through an Exceptionally Compatible Alignment-Substitution Model
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