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inferred← citeshttps://doi.org/10.11646/phytotaxa.702.2.5zenodo-depositor-declared
Circumscription of African Dipcadi (Asparagaceae, Scilloideae) species based on ITS sequence data and morphology
inferred← citeshttps://doi.org/10.11646/zootaxa.5375.3.3zenodo-depositor-declared
How complex is the Naineris setosa species complex? First integrative study of a presumed cosmopolitan and invasive annelid (Sedentaria: Orbiniidae)
inferred← citeshttps://doi.org/10.5852/ejt.2017.283zenodo-depositor-declared
Pitfalls in supermatrix phylogenomics
inferred← citeshttps://doi.org/10.1002/9780470570418.ch2openalex-snapshot
Current Approaches to Phylogenomic Reconstruction
inferred← citeshttps://doi.org/10.1007/978-1-0716-2429-6_1openalex-snapshot
Orthology Prediction and Phylogenetic Analysis Methods in Plants
inferred← citeshttps://doi.org/10.1007/978-1-4419-5913-3_27openalex-snapshot
Genome-Wide EST Data Mining Approaches to Resolving Incongruence of Molecular Phylogenies
inferred← citeshttps://doi.org/10.1007/978-3-030-16477-5_6openalex-snapshot
Resolving the Avian Tree of Life from Top to Bottom: The Promise and Potential Boundaries of the Phylogenomic Era
inferred← citeshttps://doi.org/10.1007/978-3-030-60181-2_13openalex-snapshot
Bayesian Phylogenomic Dating
inferred← citeshttps://doi.org/10.1007/978-3-319-54064-1_9openalex-snapshot
Sources of Error and Incongruence in Phylogenomic Analyses
inferred← citeshttps://doi.org/10.1007/s00335-014-9544-9openalex-snapshot
Mitochondrial data are not suitable for resolving placental mammal phylogeny
inferred← citeshttps://doi.org/10.1007/s00606-025-01947-0openalex-snapshot
Exploring the phylogenomics of Dipcadi (Asparagaceae, Scilloideae) and assessing the utility of ITS as a DNA barcode
inferred← citeshttps://doi.org/10.1007/s10531-018-1573-3openalex-snapshot
Revisiting the Darwinian shortfall in biodiversity conservation
inferred← citeshttps://doi.org/10.1007/s12064-012-0173-0openalex-snapshot
Analysis of phylogenetic signal in protostomial intron patterns using Mutual Information
inferred← citeshttps://doi.org/10.1007/s13127-019-00397-0openalex-snapshot
The phylogenomic revolution and its conceptual innovations: a text mining approach
inferred← citeshttps://doi.org/10.1016/bs.adgen.2017.09.008openalex-snapshot
Fungal Phylogeny in the Age of Genomics: Insights Into Phylogenetic Inference From Genome-Scale Datasets
inferred← citeshttps://doi.org/10.1016/j.bbrc.2007.02.048openalex-snapshot
Construction of phylogenetic profiles based on the genetic distance of hundreds of genomes
inferred← citeshttps://doi.org/10.1016/j.funbio.2012.04.009openalex-snapshot
Genome wide AFLP markers support cryptic species in Coniophora (Boletales)
inferred← citeshttps://doi.org/10.1016/j.hal.2025.102829openalex-snapshot
Comparative genomic and phylogenetic analysis of mitochondrial genomes of the Pseudo-nitzschia HAB species
inferred← citeshttps://doi.org/10.1016/j.meegid.2009.05.004openalex-snapshot
Legionella pneumophila: Population genetics, phylogeny and genomics
inferred← citeshttps://doi.org/10.1016/j.mimet.2016.09.020openalex-snapshot
Use of phylogenetical analysis to predict susceptibility of pathogenic Candida spp. to antifungal drugs
inferred← citeshttps://doi.org/10.1016/j.sajb.2013.06.012openalex-snapshot
The promise of genomics for a “next generation” of advances in higher-level legume molecular systematics
inferred← citeshttps://doi.org/10.1016/j.shpsc.2012.10.003openalex-snapshot
When integration fails: Prokaryote phylogeny and the tree of life
inferred← citeshttps://doi.org/10.1016/j.syapm.2010.03.003openalex-snapshot
En route to a genome-based classification of Archaea and Bacteria?
inferred← citeshttps://doi.org/10.1016/j.tig.2006.02.003openalex-snapshot
Phylogenomics: the beginning of incongruence?
inferred← citeshttps://doi.org/10.1016/j.tig.2026.05.003openalex-snapshot
Phylogenomics beyond the ‘bag-of-genes’ model
inferred← citeshttps://doi.org/10.1016/j.tplants.2004.08.008openalex-snapshot
Genome-scale data, angiosperm relationships, and ‘ending incongruence’: a cautionary tale in phylogenetics
inferred← citeshttps://doi.org/10.1016/j.ympev.2013.09.011openalex-snapshot
BaCoCa – A heuristic software tool for the parallel assessment of sequence biases in hundreds of gene and taxon partitions
inferred← citeshttps://doi.org/10.1016/j.ympev.2018.03.033openalex-snapshot
Filtering nucleotide sites by phylogenetic signal to noise ratio increases confidence in the Neoaves phylogeny generated from ultraconserved elements
inferred← citeshttps://doi.org/10.1016/j.ympev.2018.07.018openalex-snapshot
Phylogenomic analysis on the exceptionally diverse fish clade Gobioidei (Actinopterygii: Gobiiformes) and data-filtering based on molecular clocklikeness
inferred← citeshttps://doi.org/10.1016/j.ympev.2020.106899openalex-snapshot
Larger, unfiltered datasets are more effective at resolving phylogenetic conflict: Introns, exons, and UCEs resolve ambiguities in Golden-backed frogs (Anura: Ranidae; genus Hylarana)
inferred← citeshttps://doi.org/10.1016/j.ympev.2021.107112openalex-snapshot
Large-scale phylogenomic analysis provides new insights into the phylogeny of the class Oligohymenophorea (Protista, Ciliophora) with establishment of a new subclass Urocentria nov. subcl
inferred← citeshttps://doi.org/10.1016/j.ympev.2021.107344openalex-snapshot
Gene-tree misrooting drives conflicts in phylogenomic coalescent analyses of palaeognath birds
inferred← citeshttps://doi.org/10.1016/j.ympev.2025.108386openalex-snapshot
Discordance between phylogenomic methods in Near Eastern mountain newts (Neurergus, Salamandridae)
inferred← citeshttps://doi.org/10.1017/9781139047678.002openalex-snapshot
Introduction: Carving Nature at Its Joints, or Why Birds Are Not Dinosaurs and Men Are Not Apes
inferred← citeshttps://doi.org/10.1017/9781139047678.003openalex-snapshot
The Interrelationships of Organisms
inferred← citeshttps://doi.org/10.1017/9781139047678.006openalex-snapshot
Systematics: Exposing Myths
inferred← citeshttps://doi.org/10.1017/9781139047678.009openalex-snapshot
Monothetic and Polythetic Taxa
inferred← citeshttps://doi.org/10.1017/9781139047678.010openalex-snapshot
Non-taxa or the Absence of –Phyly: Paraphyly and Aphyly
inferred← citeshttps://doi.org/10.1017/9781139047678.012openalex-snapshot
Parameters of Classification:Ordo Ab Chao
inferred← citeshttps://doi.org/10.1017/9781139047678.013openalex-snapshot
How to Study Classification
inferred← citeshttps://doi.org/10.1017/9781139047678.014openalex-snapshot
Modern Artificial Methods and Raw Data
inferred← citeshttps://doi.org/10.1017/9781139047678.015openalex-snapshot
How to Study Classification: Consensus Techniques and General Classifications
inferred← citeshttps://doi.org/10.1017/9781139047678.016openalex-snapshot
How to Study Classification: ‘Total Evidence’ vs. ‘Consensus’, Character Congruence vs. Taxonomic Congruence, Simultaneous Analysis vs. Partitioned Data
inferred← citeshttps://doi.org/10.1017/9781139047678.017openalex-snapshot
How to Study Classification
inferred← citeshttps://doi.org/10.1017/9781139047678.018openalex-snapshot
How to Study Classification
inferred← citeshttps://doi.org/10.1017/9781139047678.020openalex-snapshot
Beyond Classification: How to Study Phylogeny
inferred← citeshttps://doi.org/10.1017/9781139047678.021openalex-snapshot
The Separation of Classification and Phylogenetics
inferred← citeshttps://doi.org/10.1017/9781139047678.022openalex-snapshot
Further Myths and More Misunderstandings
inferred← citeshttps://doi.org/10.1017/9781139047678.025openalex-snapshot
Systematics Association Special Volumes
inferred← citeshttps://doi.org/10.1017/s0953756204229586openalex-snapshot
Resolving Incongruence in Molecular Phylogenies
inferred← citeshttps://doi.org/10.1038/s41598-019-45455-xopenalex-snapshot
Multiple historical processes obscure phylogenetic relationships in a taxonomically difficult group (Lobariaceae, Ascomycota)
inferred← citeshttps://doi.org/10.1080/10242422.2022.2030317openalex-snapshot
Accurate computational evolution of proteins and its dependence on deep learning and machine learning strategies
inferred← citeshttps://doi.org/10.1080/10635150590947339openalex-snapshot
Choosing the Best Genes for the Job: The Case for Stationary Genes in Genome-Scale Phylogenetics
inferred← citeshttps://doi.org/10.1080/10635150701294733openalex-snapshot
How Many Genes Should a Systematist Sample? Conflicting Insights from a Phylogenomic Matrix Characterized by Replicated Incongruence
inferred← citeshttps://doi.org/10.1080/10635150802206883openalex-snapshot
Optimal Data Partitioning and a Test Case for Ray-Finned Fishes (Actinopterygii) Based on Ten Nuclear Loci
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/gbe/evac129openalex-snapshot
A Practical Guide to Design and Assess a Phylogenomic Study
inferred← citeshttps://doi.org/10.1093/gbe/evr095openalex-snapshot
Loss of Different Inverted Repeat Copies from the Chloroplast Genomes of Pinaceae and Cupressophytes and Influence of Heterotachy on the Evaluation of Gymnosperm Phylogeny
inferred← citeshttps://doi.org/10.1093/molbev/msaa251openalex-snapshot
Interrogating Genomic-Scale Data to Resolve Recalcitrant Nodes in the Spider Tree of Life
inferred← citeshttps://doi.org/10.1093/molbev/msab026openalex-snapshot
Genome-Scale Profiling Reveals Noncoding Loci Carry Higher Proportions of Concordant Data
inferred← citeshttps://doi.org/10.1093/molbev/msab300openalex-snapshot
Lower Statistical Support with Larger Data Sets: Insights from the Ochrophyta Radiation
inferred← citeshttps://doi.org/10.1093/molbev/msn213openalex-snapshot
The Apicomplexan Whole-Genome Phylogeny: An Analysis of Incongruence among Gene Trees
inferred← citeshttps://doi.org/10.1093/sysbio/syae056openalex-snapshot
Complex Models of Sequence Evolution Improve Fit, But Not Gene Tree Discordance, for Tetrapod Mitogenomes
inferred← citeshttps://doi.org/10.1093/sysbio/syv041openalex-snapshot
Can We Identify Genes with Increased Phylogenetic Reliability?
inferred← citeshttps://doi.org/10.1093/sysbio/syv059openalex-snapshot
Selecting Question-Specific Genes to Reduce Incongruence in Phylogenomics: A Case Study of Jawed Vertebrate Backbone Phylogeny
inferred← citeshttps://doi.org/10.1093/sysbio/syx041openalex-snapshot
Why Do Phylogenomic Data Sets Yield Conflicting Trees? Data Type Influences the Avian Tree of Life more than Taxon Sampling
inferred← citeshttps://doi.org/10.1093/sysbio/syx063openalex-snapshot
Why Concatenation Fails Near the Anomaly Zone
inferred← citeshttps://doi.org/10.1093/sysbio/syy013openalex-snapshot
Variation Across Mitochondrial Gene Trees Provides Evidence for Systematic Error: How Much Gene Tree Variation Is Biological?
inferred← citeshttps://doi.org/10.1093/sysbio/syy085openalex-snapshot
Resolving Deep Nodes in an Ancient Radiation of Neotropical Fishes in the Presence of Conflicting Signals from Incomplete Lineage Sorting
inferred← citeshttps://doi.org/10.1093/sysbio/syz019openalex-snapshot
Whole-Genome Analyses Resolve the Phylogeny of Flightless Birds (Palaeognathae) in the Presence of an Empirical Anomaly Zone
inferred← citeshttps://doi.org/10.1093/sysbio/syz029openalex-snapshot
Model Choice, Missing Data, and Taxon Sampling Impact Phylogenomic Inference of Deep Basidiomycota Relationships
inferred← citeshttps://doi.org/10.1101/170696openalex-snapshot
Multiple hidden processes complicate phylogenomic inference of deep Basidiomycota relationships
inferred← citeshttps://doi.org/10.1101/2024.09.27.615508openalex-snapshot
The topography of gene tree topology space in a plant genus with a legacy of recent polyploidy and introgression
inferred← citeshttps://doi.org/10.1101/262949openalex-snapshot
Whole-genome analyses resolve the phylogeny of flightless birds (Palaeognathae) in the presence of an empirical anomaly zone
inferred← citeshttps://doi.org/10.1101/765610openalex-snapshot
Exons, Introns, and UCEs Reveal Conflicting Phylogenomic Signals in a Rapid Radiation of Frogs (Ranidae: Hylarana )
inferred← citeshttps://doi.org/10.1109/tcbb.2017.2718507openalex-snapshot
Computing Manhattan Path-Difference Median Trees: A Practical Local Search Approach
inferred← citeshttps://doi.org/10.1111/age.12088openalex-snapshot
Phylogenetic resolution power of microsatellites and various single‐nucleotide polymorphism types assessed in 10 divergent chicken populations
inferred← citeshttps://doi.org/10.1111/anzs.12035openalex-snapshot
The Rise of Statistical Phylogenetics
inferred← citeshttps://doi.org/10.1111/eva.13565openalex-snapshot
Identifying and addressing methodological incongruence in phylogenomics: A review
inferred← citeshttps://doi.org/10.1111/jzs.12170openalex-snapshot
Inferring the phylogenetic position of theDrosophila flavopilosagroup: Incongruence within and between mitochondrial and nuclear multilocus datasets
inferred← citeshttps://doi.org/10.1111/nyas.14471openalex-snapshot
Patterns and impacts of nonvertical evolution in eukaryotes: a paradigm shift
inferred← citeshttps://doi.org/10.1142/s0219720024500082openalex-snapshot
Utilization of systematic error-assessment software to improve phylogenetic accuracy
inferred← citeshttps://doi.org/10.1145/2975167.2975209openalex-snapshot
Manhattan Path-Difference Median Trees
inferred← citeshttps://doi.org/10.1146/annurev.ecolsys.35.112202.130205openalex-snapshot
Phylogenomics
inferred← citeshttps://doi.org/10.1186/1471-2105-10-219openalex-snapshot
OrthoSelect: a protocol for selecting orthologous groups in phylogenomics
inferred← citeshttps://doi.org/10.1186/1471-2148-9-150openalex-snapshot
On the phylogenetic position of Myzostomida: Can 77 genes get it wrong?
inferred← citeshttps://doi.org/10.1186/s12859-015-0632-yopenalex-snapshot
A composite genome approach to identify phylogenetically informative data from next-generation sequencing
inferred← citeshttps://doi.org/10.1186/s12915-023-01579-1openalex-snapshot
The genome of the pygmy right whale illuminates the evolution of rorquals
inferred← citeshttps://doi.org/10.1186/s40657-020-00194-wopenalex-snapshot
Whole genome phylogeny of Gallus: introgression and data-type effects
inferred← citeshttps://doi.org/10.12688/f1000research.139356.1openalex-snapshot
Scoutknife: A naïve, whole genome informed phylogenetic robusticity metric
inferred← citeshttps://doi.org/10.12705/622.8openalex-snapshot
Legume phylogeny and classification in the 21st century: Progress, prospects and lessons for other species–rich clades
inferred← citeshttps://doi.org/10.1371/journal.pbio.1000602openalex-snapshot
Resolving Difficult Phylogenetic Questions: Why More Sequences Are Not Enough
inferred← citeshttps://doi.org/10.1371/journal.pone.0062892openalex-snapshot
The Impact of Paralogy on Phylogenomic Studies – A Case Study on Annelid Relationships
inferred← citeshttps://doi.org/10.1371/journal.pone.0183393openalex-snapshot
Can quartet analyses combining maximum likelihood estimation and Hennigian logic overcome long branch attraction in phylogenomic sequence data?
inferred← citeshttps://doi.org/10.1371/journal.pone.0202729openalex-snapshot
Noise and biases in genomic data may underlie radically different hypotheses for the position of Iguania within Squamata
inferred← citeshttps://doi.org/10.21248/gups.75018openalex-snapshot
The application of baleen whale genomes in conservation and evolutionary research
inferred← citeshttps://doi.org/10.2139/ssrn.5077292openalex-snapshot
Discordance between Phylogenomic Methods Due to Introgression in Near Eastern Mountain Newts (Neurergus, Salamandridae)
inferred← citeshttps://doi.org/10.23860/diss-ada-eren-2023openalex-snapshot
Utilization of Large-Scale Genomic Data and Phylogenetic Methods in Studying Evolutionary Radiations
inferred← citeshttps://doi.org/10.3389/fpls.2019.01773openalex-snapshot
A Phylogenomic Perspective on Evolution and Discordance in the Alpine-Arctic Plant Clade Micranthes (Saxifragaceae)
inferred← citeshttps://doi.org/10.3390/biology9040064openalex-snapshot
Phylogenetic Analyses of Sites in Different Protein Structural Environments Result in Distinct Placements of the Metazoan Root
inferred← citeshttps://doi.org/10.3390/d13110555openalex-snapshot
Protein Structure, Models of Sequence Evolution, and Data Type Effects in Phylogenetic Analyses of Mitochondrial Data: A Case Study in Birds
inferred← citeshttps://doi.org/10.3390/insects17080805openalex-snapshot
The Application of Molecular Techniques to Improve the Classification of Limoniidae
inferred← citeshttps://doi.org/10.3390/microorganisms9102014openalex-snapshot
Aspergillus fumigatus versus Genus Aspergillus: Conservation, Adaptive Evolution and Specific Virulence Genes
inferred← citeshttps://doi.org/10.4137/ebo.s14239openalex-snapshot
TreSpEx–-Detection of Misleading Signal in Phylogenetic Reconstructions Based on Tree Information
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/10.48550/arxiv.2106.01951openalex-snapshot
Accurate computational evolution of proteins and its dependence on deep learning
inferred← citeshttps://doi.org/10.6084/m9.figshare.11992323openalex-snapshot
Additional file 6 of Whole genome phylogeny of Gallus: introgression and data-type effects
inferred← citeshttps://doi.org/10.6084/m9.figshare.11992332openalex-snapshot
Additional file 7 of Whole genome phylogeny of Gallus: introgression and data-type effects
inferred← citeshttps://doi.org/10.6084/m9.figshare.11992338openalex-snapshot
Additional file 8 of Whole genome phylogeny of Gallus: introgression and data-type effects
inferred← citeshttps://doi.org/10.70675/9c8d2b6cz53cfz4351za1cbz83d9c20217f1openalex-snapshot
Impact des violations des modèles d'annotation et d'évolution de séquences en phylogénomique : application à l'étude des eucaryotes photosynthétiques
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