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The Impact of Outgroup Choice and Missing Data on Major Seed Plant Phylogenetics Using Genome-Wide EST Data
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
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PAUP * [Phylogenetic Analysis Using Parsimony (and Other Methods)]
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Corroboration among Data Sets in Simultaneous Analysis: Hidden Support for Phylogenetic Relationships among Higher Level Artiodactyl Taxa
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Molecules, Morphology, Fossils, and the Relationship of Angiosperms and Gnetales
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Noise and Incongruence: Interpreting Results of the Incongruence Length Difference Test
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Exploiting Fine-Grained Parallelism in the Phylogenetic Likelihood Function with MPI, Pthreads, and OpenMP: A Performance Study
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Phylogeny of gymnosperms inferred fromrbcL gene sequences
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Seed plant phylogeny and the origin of angiosperms: An experimental cladistic approach
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Molecular Data from the Chloroplast rpoC1 Gene Suggest a Deep and Distinct Dichotomy of Contemporary Spermatophytes into Two Monophyla: Gymnosperms (Including Gnetales) and Angiosperms
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The Evolution of Gymnosperms Redrawn by Phytochrome Genes: The Gnetatae Appear at the Base of the Gymnosperms
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Phylogenomics: the beginning of incongruence?
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Genome-scale data, angiosperm relationships, and ‘ending incongruence’: a cautionary tale in phylogenetics
inferredcites →https://doi.org/10.1016/j.tplants.2005.03.006openalex-snapshot
The place of Amborella within the radiation of angiosperms
inferredcites →https://doi.org/10.1016/s0076-6879(05)95008-8openalex-snapshot
Animal Phylogenomics: Multiple Interspecific Genome Comparisons
inferredcites →https://doi.org/10.1016/s0960-9822(00)00304-3openalex-snapshot
Seed plant phylogeny: Demise of the anthophyte hypothesis?
inferredcites →https://doi.org/10.1016/s1055-7903(03)00207-0openalex-snapshot
The major clades of MADS-box genes and their role in the development and evolution of flowering plants
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How can we deliver the large plant genomes? Strategies and perspectives
inferredcites →https://doi.org/10.1038/46528openalex-snapshot
Angiosperm phylogeny inferred from multiple genes as a tool for comparative biology
inferredcites →https://doi.org/10.1038/nature01644openalex-snapshot
Sequencing and comparison of yeast species to identify genes and regulatory elements
inferredcites →https://doi.org/10.1038/nature02053openalex-snapshot
Genome-scale approaches to resolving incongruence in molecular phylogenies
inferredcites →https://doi.org/10.1038/nature06614openalex-snapshot
Broad phylogenomic sampling improves resolution of the animal tree of life
inferredcites →https://doi.org/10.1038/ng1154openalex-snapshot
The Widespread Colonization Island of Actinobacillus actinomycetemcomitans
inferredcites →https://doi.org/10.1073/pnas.96.13.7342openalex-snapshot
MADS-box genes reveal that gnetophytes are more closely related to conifers than to flowering plants
inferredcites →https://doi.org/10.1073/pnas.97.8.4086openalex-snapshot
Seed plant phylogeny inferred from all three plant genomes: Monophyly of extant gymnosperms and origin of Gnetales from conifers
inferredcites →https://doi.org/10.1073/pnas.97.8.4092openalex-snapshot
Phylogeny of seed plants based on all three genomic compartments: Extant gymnosperms are monophyletic and Gnetales' closest relatives are conifers
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The Utility of the Incongruence Length Difference Test
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Missing Data, Incomplete Taxa, and Phylogenetic Accuracy
inferredcites →https://doi.org/10.1080/10635150490264752openalex-snapshot
Congruence Versus Phylogenetic Accuracy: Revisiting the Incongruence Length Difference Test
inferredcites →https://doi.org/10.1080/10635150590945368openalex-snapshot
Hidden Likelihood Support in Genomic Data: Can Forty-Five Wrongs Make a Right?
inferredcites →https://doi.org/10.1080/10635150701294733openalex-snapshot
How Many Genes Should a Systematist Sample? Conflicting Insights from a Phylogenomic Matrix Characterized by Replicated Incongruence
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A Rapid Bootstrap Algorithm for the RAxML Web Servers
inferredcites →https://doi.org/10.1093/bioinformatics/8.3.275openalex-snapshot
The rapid generation of mutation data matrices from protein sequences
inferredcites →https://doi.org/10.1093/bioinformatics/bti263openalex-snapshot
ProtTest: selection of best-fit models of protein evolution
inferredcites →https://doi.org/10.1093/bioinformatics/btk040openalex-snapshot
OrthologID: automation of genome-scale ortholog identification within a parsimony framework
inferredcites →https://doi.org/10.1093/bioinformatics/btl446openalex-snapshot
RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
inferredcites →https://doi.org/10.1093/bioinformatics/btl496openalex-snapshot
Sungear: interactive visualization and functional analysis of genomic datasets
inferredcites →https://doi.org/10.1093/molbev/msh182openalex-snapshot
Phylogenomics of Eukaryotes: Impact of Missing Data on Large Alignments
inferredcites →https://doi.org/10.1093/molbev/msi111openalex-snapshot
Multigene Analyses of Bilaterian Animals Corroborate the Monophyly of Ecdysozoa, Lophotrochozoa, and Protostomia
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a004098openalex-snapshot
When Does the Incongruence Length Difference Test Fail?
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a025597openalex-snapshot
Noncoding sequences from the slowly evolving chloroplast inverted repeat in addition to rbcL data do not support gnetalean affinities of angiosperms
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a026089openalex-snapshot
The phylogeny of land plants inferred from 18S rDNA sequences: pushing the limits of rDNA signal?
inferredcites →https://doi.org/10.1093/sysbio/44.4.570openalex-snapshot
Constructing a Significance Test for Incongruence
inferredcites →https://doi.org/10.1093/sysbio/46.4.654openalex-snapshot
Multiple Sources of Character Information and the Phylogeny of Hawaiian Drosophilids
inferredcites →https://doi.org/10.1098/rstb.2008.0163openalex-snapshot
Efficient computation of the phylogenetic likelihood function on multi-gene alignments and multi-core architectures
inferredcites →https://doi.org/10.1109/ipdps.2006.1639535openalex-snapshot
Phylogenetic models of rate heterogeneity: a high performance computing perspective
inferredcites →https://doi.org/10.1111/j.1096-0031.1990.tb00550.xopenalex-snapshot
NUCLEIC ACID SEQUENCE PHYLOGENY AND RANDOM OUTGROUPS
inferredcites →https://doi.org/10.1111/j.1096-0031.1994.tb00179.xopenalex-snapshot
BRANCH SUPPORT AND TREE STABILITY
inferredcites →https://doi.org/10.1111/j.1096-0031.1994.tb00181.xopenalex-snapshot
TESTING SIGNIFICANCE OF INCONGRUENCE
inferredcites →https://doi.org/10.1111/j.1558-5646.1990.tb03855.xopenalex-snapshot
ACCURACY OF ESTIMATED PHYLOGENIES: EFFECTS OF TREE TOPOLOGY AND EVOLUTIONARY MODEL
inferredcites →https://doi.org/10.1126/science.1068037openalex-snapshot
A Draft Sequence of the Rice Genome ( Oryza sativa L. ssp. indica )
inferredcites →https://doi.org/10.1126/science.1068275openalex-snapshot
A Draft Sequence of the Rice Genome ( Oryza sativa L. ssp. japonica )
inferredcites →https://doi.org/10.1145/1362622.1362628openalex-snapshot
Large-scale maximum likelihood-based phylogenetic analysis on the IBM BlueGene/L
inferredcites →https://doi.org/10.1186/1471-2105-9-103openalex-snapshot
Automated simultaneous analysis phylogenetics (ASAP): an enabling tool for phlyogenomics
inferredcites →https://doi.org/10.1186/1471-2148-6-48openalex-snapshot
ESTimating plant phylogeny: lessons from partitioning
inferredcites →https://doi.org/10.1186/1471-2229-5-5openalex-snapshot
Floral gene resources from basal angiosperms for comparative genomics research
inferredcites →https://doi.org/10.1554/04-565.1openalex-snapshot
ANGIOSPERM DIVERGENCE TIMES: THE EFFECT OF GENES, CODON POSITIONS, AND TIME CONSTRAINTS
inferredcites →https://doi.org/10.2307/2399221openalex-snapshot
Phylogenetic Analysis of Seed Plants and the Origin of Angiosperms
inferredcites →https://doi.org/10.2307/2399846openalex-snapshot
Phylogenetics of Seed Plants: An Analysis of Nucleotide Sequences from the Plastid Gene rbcL
inferredcites →https://doi.org/10.2307/2399901openalex-snapshot
A Reevaluation of Seed Plant Phylogeny
inferredcites →https://doi.org/10.2307/2399902openalex-snapshot
Functional Constraints and rbcL Evidence for Land Plant Phylogeny
inferredcites →https://doi.org/10.2307/2419767openalex-snapshot
Lignophyte Phylogeny and the Evolution of Spermatophytes: A Numerical Cladistic Analysis
inferredcites →https://doi.org/10.2307/2666635openalex-snapshot
The Mostly Male Theory of Flower Evolutionary Origins: From Genes to Fossils
inferredcites →https://doi.org/10.3732/ajb.0800178openalex-snapshot
Phylogenetic relationships among seed plants: Persistent questions and the limits of molecular data
inferredcites →https://doi.org/10.3732/ajb.89.10.1670openalex-snapshot
Phylogeny of seed plants based on evidence from eight genes
inferredcites →https://doi.org/10.3732/ajb.91.10.1656openalex-snapshot
Molecular evidence on plant divergence times
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
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Evolution and biogeography of gymnosperms
inferred← citeshttps://doi.org/10.1016/j.ympev.2014.08.006openalex-snapshot
Should genes with missing data be excluded from phylogenetic analyses?
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inferred← citeshttps://doi.org/10.1016/j.ympev.2020.107065openalex-snapshot
Diverse phylogenomic datasets uncover a concordant scenario of laurasiatherian interordinal relationships
inferred← citeshttps://doi.org/10.1016/j.ympev.2023.107806openalex-snapshot
Multiple outgroups can cause random rooting in phylogenomics
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Phylogenomics reveals taxonomic challenges in Calibrachoa (Solanaceae) and sheds light on the origins of cultivated million bells
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Molecules, Morphology, Fossils and the Origination and Extinction Dynamics of Scleractinian Corals
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Phylotranscriptomic analysis of the origin and early diversification of land plants
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The morphophysiological dormancy inAmborella trichopodaseeds is a pleisiomorphic trait in angiosperms
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The impact of taxon sampling on phylogenetic inference: a review of two decades of controversy
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Large Phylogenomic Data sets Reveal Deep Relationships and Trait Evolution in Chlorophyte Green Algae
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Using Phylogenomic Patterns and Gene Ontology to Identify Proteins of Importance in Plant Evolution
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Loss of Different Inverted Repeat Copies from the Chloroplast Genomes of Pinaceae and Cupressophytes and Influence of Heterotachy on the Evaluation of Gymnosperm Phylogeny
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Peer Review #1 of "A 250 plastome phylogeny of the grass family (Poaceae): topological support under different data partitions (v0.1)"
inferred← citeshttps://doi.org/10.7287/peerj.4299v0.1/reviews/2openalex-snapshot
Peer Review #2 of "A 250 plastome phylogeny of the grass family (Poaceae): topological support under different data partitions (v0.1)"
inferred← citeshttps://doi.org/10.7287/peerj.4299v0.1/reviews/3openalex-snapshot
Peer Review #3 of "A 250 plastome phylogeny of the grass family (Poaceae): topological support under different data partitions (v0.1)"
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Peer Review #2 of "A 250 plastome phylogeny of the grass family (Poaceae): topological support under different data partitions (v0.2)"
inferred← citeshttps://doi.org/10.7287/peerj.4299v0.2/reviews/3openalex-snapshot
Peer Review #3 of "A 250 plastome phylogeny of the grass family (Poaceae): topological support under different data partitions (v0.2)"
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Phylogenetics within Camassia (Asparagaceae): examining difficult taxonomy and unusual variation using genomic restriction-site-associated DNA sequencing data
inferred← citeshttps://doi.org/10.7717/peerj.4299openalex-snapshot
A 250 plastome phylogeny of the grass family (Poaceae): topological support under different data partitions
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