On the public citation graph

Phylogenetic Synecdoche Demonstrates Optimality of Subsampling and Improves Recovery of the Blaberoidea Phylogeny

https://doi.org/10.1101/601237
0 signed · 94 inferred · view as graph

Inferred edges come from two machine sources: sweeps of open repository metadata (mostly SSRN and Zenodo), and a bulk OpenAlex citation snapshot. Every row below is labelled with the one it came from. Neither is a complete citation index — absence here is not evidence of absence.

Is this your work? Sign in with ORCID and put your name on the claims that are yours.
Claim with ORCID
Reference health. See whether every reference in this work resolves to a known work and none has been retracted — and get a dated CiteStamped badge you can embed.
See reference health

What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/ajb2.1016openalex-snapshot
Quartet Sampling distinguishes lack of support from conflicting support in the green plant tree of life
inferredcites →https://doi.org/10.1016/0025-5564(81)90043-2openalex-snapshot
Comparison of phylogenetic trees
inferredcites →https://doi.org/10.1016/j.asd.2018.05.002openalex-snapshot
Reanalyzing the Palaeoptera problem – The origin of insect flight remains obscure
inferredcites →https://doi.org/10.1016/j.jtbi.2017.02.037openalex-snapshot
The optimal rate for resolving a near-polytomy in a phylogeny
inferredcites →https://doi.org/10.1016/j.mbs.2013.09.004openalex-snapshot
Weighted relative entropy for phylogenetic tree based on 2-step Markov Model
inferredcites →https://doi.org/10.1016/j.ympev.2014.06.013openalex-snapshot
A hybrid phylogenetic–phylogenomic approach for species tree estimation in African Agama lizards with applications to biogeography, character evolution, and diversification
inferredcites →https://doi.org/10.1016/j.ympev.2014.08.019openalex-snapshot
Identifying possible sister groups of Cryptocercidae+Isoptera: A combined molecular and morphological phylogeny of Dictyoptera
inferredcites →https://doi.org/10.1016/j.ympev.2015.05.027openalex-snapshot
Genome-wide ultraconserved elements exhibit higher phylogenetic informativeness than traditional gene markers in percomorph fishes
inferredcites →https://doi.org/10.1016/j.ympev.2018.05.007openalex-snapshot
Topological support and data quality can only be assessed through multiple tests in reviewing Blattodea phylogeny
inferredcites →https://doi.org/10.1016/j.ympev.2018.10.001openalex-snapshot
Gene-wise resampling outperforms site-wise resampling in phylogenetic coalescence analyses
inferredcites →https://doi.org/10.1038/nbt.1883openalex-snapshot
Full-length transcriptome assembly from RNA-Seq data without a reference genome
inferredcites →https://doi.org/10.1038/nmeth.4285openalex-snapshot
ModelFinder: fast model selection for accurate phylogenetic estimates
inferredcites →https://doi.org/10.1038/nprot.2013.084openalex-snapshot
De novo transcript sequence reconstruction from RNA-Seq: reference generation and analysis with Trinity
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/10.1038/s41598-017-04243-1openalex-snapshot
Reconstructing the phylogeny of Blattodea: robust support for interfamilial relationships and major clades
inferredcites →https://doi.org/10.1038/srep41926openalex-snapshot
Limb proportions show developmental plasticity in response to embryo movement
inferredcites →https://doi.org/10.1073/pnas.1817794116openalex-snapshot
Evolutionary history of Polyneoptera and its implications for our understanding of early winged insects
inferredcites →https://doi.org/10.1073/pnas.94.13.6815openalex-snapshot
Likelihood-mapping: A simple method to visualize phylogenetic content of a sequence alignment
inferredcites →https://doi.org/10.1080/10635150600865567openalex-snapshot
Detecting the Node-Density Artifact in Phylogeny Reconstruction
inferredcites →https://doi.org/10.1080/10635150701311362openalex-snapshot
Profiling Phylogenetic Informativeness
inferredcites →https://doi.org/10.1080/106351599260409openalex-snapshot
Stability of Cladistic Relationships between Cetacea and Higher-Level Artiodactyl Taxa
inferredcites →https://doi.org/10.1093/bioinformatics/btp348openalex-snapshot
trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses
inferredcites →https://doi.org/10.1093/bioinformatics/btq706openalex-snapshot
phangorn: phylogenetic analysis in R
inferredcites →https://doi.org/10.1093/bioinformatics/btu033openalex-snapshot
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
inferredcites →https://doi.org/10.1093/bioinformatics/btu531openalex-snapshot
AliView: a fast and lightweight alignment viewer and editor for large datasets
inferredcites →https://doi.org/10.1093/gbe/evr121openalex-snapshot
Random Addition Concatenation Analysis: A Novel Approach to the Exploration of Phylogenomic Signal Reveals Strong Agreement between Core and Shell Genomic Partitions in the Cyanobacteria
inferredcites →https://doi.org/10.1093/gbe/evs104openalex-snapshot
Insect Phylogenomics: Exploring the Source of Incongruence Using New Transcriptomic Data
inferredcites →https://doi.org/10.1093/gbe/evt157openalex-snapshot
Phylotranscriptomics: Saturated Third Codon Positions Radically Influence the Estimation of Trees Based on Next-Gen Data
inferredcites →https://doi.org/10.1093/molbev/mss020openalex-snapshot
PartitionFinder: Combined Selection of Partitioning Schemes and Substitution Models for Phylogenetic Analyses
inferredcites →https://doi.org/10.1093/molbev/mst010openalex-snapshot
MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
inferredcites →https://doi.org/10.1093/molbev/mst196openalex-snapshot
Decisive Data Sets in Phylogenomics: Lessons from Studies on the Phylogenetic Relationships of Primarily Wingless Insects
inferredcites →https://doi.org/10.1093/molbev/msu300openalex-snapshot
IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies
inferredcites →https://doi.org/10.1093/molbev/msv003openalex-snapshot
The Relationship between dN/dS and Scaled Selection Coefficients
inferredcites →https://doi.org/10.1093/molbev/msv266openalex-snapshot
The Impact of Missing Data on Species Tree Estimation
inferredcites →https://doi.org/10.1093/molbev/msw040openalex-snapshot
Computing the Internode Certainty and Related Measures from Partial Gene Trees
inferredcites →https://doi.org/10.1093/molbev/msw056openalex-snapshot
BaitFisher: A Software Package for Multispecies Target DNA Enrichment Probe Design
inferredcites →https://doi.org/10.1093/molbev/msw260openalex-snapshot
PartitionFinder 2: New Methods for Selecting Partitioned Models of Evolution for Molecular and Morphological Phylogenetic Analyses
inferredcites →https://doi.org/10.1093/molbev/msx313openalex-snapshot
MBE Citation Classics (2018 Edition)
inferredcites →https://doi.org/10.1093/molbev/msy013openalex-snapshot
Transoceanic Dispersal and Plate Tectonics Shaped Global Cockroach Distributions: Evidence from Mitochondrial Phylogenomics
inferredcites →https://doi.org/10.1093/molbev/msy222openalex-snapshot
Population Genetics Based Phylogenetics Under Stabilizing Selection for an Optimal Amino Acid Sequence: A Nested Modeling Approach
inferredcites →https://doi.org/10.1093/nar/gks1116openalex-snapshot
OrthoDB: a hierarchical catalog of animal, fungal and bacterial orthologs
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a040152openalex-snapshot
A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome.
inferredcites →https://doi.org/10.1093/sysbio/syr064openalex-snapshot
A Method for Inferring the Rate of Evolution of Homologous Characters that Can Potentially Improve Phylogenetic Inference, Resolve Deep Divergence and Correct Systematic Biases
inferredcites →https://doi.org/10.1093/sysbio/sys049openalex-snapshot
Anchored Hybrid Enrichment for Massively High-Throughput Phylogenomics
inferredcites →https://doi.org/10.1093/sysbio/sys078openalex-snapshot
Pruning Rogue Taxa Improves Phylogenetic Accuracy: An Efficient Algorithm and Webservice
inferredcites →https://doi.org/10.1093/sysbio/syt109openalex-snapshot
Conflicting Phylogenies for Early Land Plants are Caused by Composition Biases among Synonymous Substitutions
inferredcites →https://doi.org/10.1093/sysbio/syu085openalex-snapshot
Practical Performance of Tree Comparison Metrics
inferredcites →https://doi.org/10.1093/sysbio/syv033openalex-snapshot
Current Methods for Automated Filtering of Multiple Sequence Alignments Frequently Worsen Single-Gene Phylogenetic Inference
inferredcites →https://doi.org/10.1093/sysbio/syv041openalex-snapshot
Can We Identify Genes with Increased Phylogenetic Reliability?
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/syw042openalex-snapshot
Estimating Bayesian Phylogenetic Information Content
inferredcites →https://doi.org/10.1093/sysbio/syw101openalex-snapshot
Bayes factors unmask highly variable information content, bias, and extreme influence in phylogenomic analyses
inferredcites →https://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
inferredcites →https://doi.org/10.1093/sysbio/syx051openalex-snapshot
More on the Best Evolutionary Rate for Phylogenetic Analysis
inferredcites →https://doi.org/10.1093/sysbio/syx058openalex-snapshot
Conserved Nonexonic Elements: A Novel Class of Marker for Phylogenomics
inferredcites →https://doi.org/10.1093/sysbio/syx070openalex-snapshot
Conflicting Evolutionary Histories of the Mitochondrial and Nuclear Genomes in New World Myotis Bats
inferredcites →https://doi.org/10.1093/sysbio/syx077openalex-snapshot
To Include or Not to Include: The Impact of Gene Filtering on Species Tree Estimation Methods
inferredcites →https://doi.org/10.1093/sysbio/syy047openalex-snapshot
Optimal Rates for Phylogenetic Inference and Experimental Design in the Era of Genome-Scale Data Sets
inferredcites →https://doi.org/10.1093/sysbio/syy088openalex-snapshot
Convergent Evolution of the Army Ant Syndrome and Congruence in Big-Data Phylogenetics
inferredcites →https://doi.org/10.1098/rspb.2018.2076openalex-snapshot
An integrative phylogenomic approach illuminates the evolutionary history of cockroaches and termites (Blattodea)
inferredcites →https://doi.org/10.1098/rstb.2003.1447openalex-snapshot
The promise of a DNA taxonomy
inferredcites →https://doi.org/10.1101/gr.4305906openalex-snapshot
Mutation hot spots in mammalian mitochondrial DNA
inferredcites →https://doi.org/10.1109/gce.2010.5676129openalex-snapshot
Creating the CIPRES Science Gateway for inference of large phylogenetic trees
inferredcites →https://doi.org/10.1111/j.1558-5646.2007.00188.xopenalex-snapshot
THE LIKELIHOOD NODE DENSITY EFFECT AND CONSEQUENCES FOR EVOLUTIONARY STUDIES OF MOLECULAR RATES
inferredcites →https://doi.org/10.1111/zsc.12210openalex-snapshot
Phylogenomic subsampling: a brief review
inferredcites →https://doi.org/10.1126/science.1257570openalex-snapshot
Phylogenomics resolves the timing and pattern of insect evolution
inferredcites →https://doi.org/10.1146/annurev.ecolsys.36.102003.152633openalex-snapshot
Model Selection in Phylogenetics
inferredcites →https://doi.org/10.11646/zootaxa.3703.1.10openalex-snapshot
Order Blattodea. In: Zhang, Z.-Q. (Ed.) Animal Biodiversity: An Outline of Higher-level Classification and Survey of Taxonomic Richness (Addenda 2013)
inferredcites →https://doi.org/10.1186/1471-2105-10-421openalex-snapshot
BLAST+: architecture and applications
inferredcites →https://doi.org/10.1186/1471-2148-11-1openalex-snapshot
Phylogenomic reconstruction of lactic acid bacteria: an update
inferredcites →https://doi.org/10.1186/1471-2148-11-369openalex-snapshot
Detecting the symplesiomorphy trap: a multigene phylogenetic analysis of terebelliform annelids
inferredcites →https://doi.org/10.1186/1471-2148-14-82openalex-snapshot
Selecting optimal partitioning schemes for phylogenomic datasets
inferredcites →https://doi.org/10.1186/1471-2148-7-1openalex-snapshot
Differential impact of simultaneous migration on coevolving hosts and parasites.
inferredcites →https://doi.org/10.1186/1471-2148-7-147openalex-snapshot
Visualizing differences in phylogenetic information content of alignments and distinction of three classes of long-branch effects
inferredcites →https://doi.org/10.1186/1471-2148-7-8openalex-snapshot
Site specific rates of mitochondrial genomes and the phylogeny of eutheria.
inferredcites →https://doi.org/10.1186/1741-7007-9-91openalex-snapshot
Difficult phylogenetic questions: more data, maybe; better methods, certainly
inferredcites →https://doi.org/10.1186/1748-7188-9-1openalex-snapshot
A minimum-labeling approach for reconstructing protein networks across multiple conditions
inferredcites →https://doi.org/10.1186/s12859-017-1529-8openalex-snapshot
Orthograph: a versatile tool for mapping coding nucleotide sequences to clusters of orthologous genes
inferredcites →https://doi.org/10.1186/s12862-015-0283-7openalex-snapshot
Automatic selection of partitioning schemes for phylogenetic analyses using iterative k-means clustering of site rates
inferredcites →https://doi.org/10.1186/s12862-015-0318-0openalex-snapshot
Evaluating the performance of anchored hybrid enrichment at the tips of the tree of life: a phylogenetic analysis of Australian Eugongylus group scincid lizards
inferredcites →https://doi.org/10.1186/s12862-016-0837-3openalex-snapshot
PhyInformR: phylogenetic experimental design and phylogenomic data exploration in R
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/10.1186/s13015-014-0022-4openalex-snapshot
A priori assessment of data quality in molecular phylogenetics
inferredcites →https://doi.org/10.1214/ss/1063994980openalex-snapshot
Applying the Bootstrap in Phylogeny Reconstruction
inferredcites →https://doi.org/10.1371/journal.pone.0035495openalex-snapshot
Perceptions and Experiences of Research Participants on Gender-Based Violence Community Based Survey: Implications for Ethical Guidelines
inferredcites →https://doi.org/10.1371/journal.pone.0036593openalex-snapshot
Long Branch Effects Distort Maximum Likelihood Phylogenies in Simulations Despite Selection of the Correct Model
inferredcites →https://doi.org/10.1371/journal.pone.0048990openalex-snapshot
A Phylogenomic Approach to Vertebrate Phylogeny Supports a Turtle-Archosaur Affinity and a Possible Paraphyletic Lissamphibia
inferredcites →https://doi.org/10.1371/journal.pone.0130127openalex-snapshot
Phylogeny of Dictyoptera: Dating the Origin of Cockroaches, Praying Mantises and Termites with Molecular Data and Controlled Fossil Evidence
inferredcites →https://doi.org/10.4137/ebo.s14239openalex-snapshot
TreSpEx–-Detection of Misleading Signal in Phylogenetic Reconstructions Based on Tree Information
inferredcites →https://doi.org/10.5812/ijem.3505openalex-snapshot
Normality Tests for Statistical Analysis: A Guide for Non-Statisticians
inferredcites →https://doi.org/10.5852/ejt.2017.291openalex-snapshot
Molecular phylogeny of Blaberidae (Dictyoptera, Blattodea) with implications for taxonomy and evolutionary studies
inferredcites →https://doi.org/10.7287/peerj.preprints.26449v2openalex-snapshot
Embracing heterogeneity: Building the Tree of Life and the future of phylogenomics
inferredcites →https://doi.org/10.7717/peerj.6399openalex-snapshot
Embracing heterogeneity: coalescing the Tree of Life and the future of phylogenomics

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1101/717660openalex-snapshot
The Implications of Over-Estimating Gene Tree Discordance on a Rapid-Radiation Species Tree (Blattodea: Blaberidae)
Editorial review for independent work. ICSAC — the Institute for Complexity Science and Advanced Computing — runs a structured editorial panel for researchers publishing outside journals, and publishes on CiteStamp rails. Submission is free and goes through ORCID: icsacinstitute.org/submit.