On the public citation graph

Efficiencies of the NJp, Maximum Likelihood, and Bayesian Methods of Phylogenetic Construction for Compositional and Noncompositional Genes

0 signed · 89 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 See whether every reference in this work resolves to a known work and none has been retracted — and get a dated CiteStamped badge you can embed.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/10.1002/0471650129.dob0534openalex-snapshot

PHYLIP (Phylogeny Inference Package)

inferredcites →https://doi.org/10.1007/bf01734359openalex-snapshot

Evolutionary trees from DNA sequences: A maximum likelihood approach

inferredcites →https://doi.org/10.1007/bf01840887openalex-snapshot

Accuracy of estimated phylogenetic trees from molecular data

inferredcites →https://doi.org/10.1007/bf02101694openalex-snapshot

Dating of the human-ape splitting by a molecular clock of mitochondrial DNA

inferredcites →https://doi.org/10.1016/0025-5564(81)90043-2openalex-snapshot

Comparison of phylogenetic trees

inferredcites →https://doi.org/10.1016/j.tpb.2014.12.005openalex-snapshot

Likelihood-based tree reconstruction on a concatenation of aligned sequence data sets can be statistically inconsistent

inferredcites →https://doi.org/10.1016/s0378-1119(00)19801-4openalex-snapshot

Preface

inferredcites →https://doi.org/10.1073/pnas.0404206101openalex-snapshot

Prospects for inferring very large phylogenies by using the neighbor-joining method

inferredcites →https://doi.org/10.1073/pnas.191248498openalex-snapshot

Incomplete taxon sampling is not a problem for phylogenetic inference

inferredcites →https://doi.org/10.1073/pnas.97.20.10866openalex-snapshot

Purifying selection and birth-and-death evolution in the ubiquitin gene family

inferredcites →https://doi.org/10.1080/10635150118469openalex-snapshot

Selecting the Best-Fit Model of Nucleotide Substitution

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/10.1093/bioinformatics/btg180openalex-snapshot

MrBayes 3: Bayesian phylogenetic inference under mixed models

inferredcites →https://doi.org/10.1093/molbev/msl072openalex-snapshot

Neighbor-Joining Revealed

inferredcites →https://doi.org/10.1093/molbev/msm088openalex-snapshot

PAML 4: Phylogenetic Analysis by Maximum Likelihood

inferredcites →https://doi.org/10.1093/oso/9780195135848.001.0001openalex-snapshot

Molecular Evolution and Phylogenetics

inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a004109openalex-snapshot

Efficient Biased Estimation of Evolutionary Distances When Substitution Rates Vary Across Sites

inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a025613openalex-snapshot

Efficiencies of different genes and different tree-building methods in recovering a known vertebrate phylogeny

inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a026408openalex-snapshot

Efficiencies of Fast Algorithms of Phylogenetic Inference Under the Criteria of Maximum Parsimony, Minimum Evolution, and Maximum Likelihood When a Large Number of Sequences Are Used

inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a040020openalex-snapshot

A Simple Method to Improve the Reliability of Tree Reconstructions

inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a040056openalex-snapshot

Theoretical foundation of the minimum-evolution method of phylogenetic inference.

inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a040108openalex-snapshot

Relative efficiencies of the maximum-likelihood, neighbor-joining, and maximum-parsimony methods when substitution rate varies with site.

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/oxfordjournals.molbev.a040127openalex-snapshot

Divergent evolution and evolution by the birth-and-death process in the immunoglobulin VH gene family.

inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a040432openalex-snapshot

Accuracy of phylogenetic trees estimated from DNA sequence data.

inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a040454openalex-snapshot

The neighbor-joining method: a new method for reconstructing phylogenetic trees.

inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a040527openalex-snapshot

A note on the neighbor-joining algorithm of Saitou and Nei.

inferredcites →https://doi.org/10.1093/sysbio/20.4.406openalex-snapshot

Toward Defining the Course of Evolution: Minimum Change for a Specific Tree Topology

inferredcites →https://doi.org/10.1093/sysbio/34.1.75openalex-snapshot

The Use of Tree Comparison Metrics

inferredcites →https://doi.org/10.1099/ijs.0.01472-0openalex-snapshot

Caloramator viterbensis sp. nov., a novel thermophilic, glycerol-fermenting bacterium isolated from a hot spring in Italy

inferredcites →https://doi.org/10.1109/tcbb.2009.32openalex-snapshot

Computing the Distribution of a Tree Metric

inferredcites →https://doi.org/10.1126/science.267.5195.255openalex-snapshot

Response : Assessing Molecular Phylogenies

inferredcites →https://doi.org/10.1126/science.7809633openalex-snapshot

Assessing Molecular Phylogenies

inferredcites →https://doi.org/10.1146/annurev.genet.39.073003.112240openalex-snapshot

Concerted and Birth-and-Death Evolution of Multigene Families

inferredcites →https://doi.org/10.2307/2529676openalex-snapshot

Minimum Mutation Fits to a Given Tree

What points at this work

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

inferred← citeshttps://doi.org/10.11646/zootaxa.5618.1.3zenodo-depositor-declared

A review of the Ocaria arpoxais species group (Lycaenidae: Theclinae) with the description of a new species previously confused with O. cinerea (Lathy)

inferred← citeshttps://doi.org/10.1002/aps3.11440openalex-snapshot

Single‐nucleotide polymorphisms that uniquely identify cultivars of avocado (Persea americana)

inferred← citeshttps://doi.org/10.1002/yea.3812openalex-snapshot

Phylogenies in yeast species descriptions: In defense of neighbor‐joining

inferred← citeshttps://doi.org/10.1007/978-3-031-21175-1_14openalex-snapshot

Phylogeny Trees as a Tool to Compare Inference Algorithms of Orthologs

inferred← citeshttps://doi.org/10.1007/978-3-319-67156-7_14openalex-snapshot

Application of Bioinformatics in Understanding of Plant Stress Tolerance

inferred← citeshttps://doi.org/10.1007/s00709-025-02118-1openalex-snapshot

Tobacco two-pore calcium channel 1a is localised at the tonoplast, but acts on events at the plasma membrane

inferred← citeshttps://doi.org/10.1007/s11033-025-10245-4openalex-snapshot

Population genetic structure of Uroteuthis edulis in the East China Sea based on the COI gene

inferred← citeshttps://doi.org/10.1016/b978-0-443-31554-1.00018-2openalex-snapshot

The evolution of genome mining tools in microbes and the role of integrated approach in search for novel drug targets

inferred← citeshttps://doi.org/10.1016/j.foodcont.2023.110034openalex-snapshot

Development of a PCR-based lateral flow immunoassay for the identification of rainbow trout ingredient in foods

inferred← citeshttps://doi.org/10.1016/j.genrep.2021.101492openalex-snapshot

Estimating antigenic distances between GII.4 human norovirus strains

inferred← citeshttps://doi.org/10.1016/j.genrep.2022.101709openalex-snapshot

Co-evolving pairs of complementary nucleotide sequence regions containing compensatory divergences and polymorphisms in rotavirus genomes

inferred← citeshttps://doi.org/10.1016/j.genrep.2023.101786openalex-snapshot

Shared clusters between phylogenetic trees for upstream and downstream regions of recombination hotspot in norovirus genomes

inferred← citeshttps://doi.org/10.1016/j.genrep.2023.101875openalex-snapshot

Classification of sapoviruses based on comparison of phylogenetic trees for structural and non-structural proteins

inferred← citeshttps://doi.org/10.1016/j.genrep.2024.101956openalex-snapshot

Shared clusters between phylogenetic trees for genomic segments of Rotavirus A with distinct genotype constellations

inferred← citeshttps://doi.org/10.1016/j.genrep.2024.102063openalex-snapshot

Intra-segmental recombinations between avian and mammalian VP4 genotypes in Rotavirus alphagastroenteritidis

inferred← citeshttps://doi.org/10.1016/j.genrep.2025.102233openalex-snapshot

Detecting signatures of episodic positive selection based on observed amino acids in hemagglutinin of H3N2 human influenza A virus

inferred← citeshttps://doi.org/10.1016/j.jtbi.2016.11.005openalex-snapshot

Species tree estimation using Neighbor Joining

inferred← citeshttps://doi.org/10.1016/j.mgene.2020.100785openalex-snapshot

Methods for making multiple alignment of genomic sequences for severe acute respiratory syndrome coronavirus 2

inferred← citeshttps://doi.org/10.1016/j.mgene.2020.100828openalex-snapshot

Effect of N-linked glycosylation at position 162 of hemagglutinin in influenza A virus A(H1N1)pdm09

inferred← citeshttps://doi.org/10.1016/j.plaphy.2023.107891openalex-snapshot

Genome-wide characterization of SINA E3 ubiquitin ligase family members and their expression profiles in response to various abiotic stresses and hormones in kiwifruit

inferred← citeshttps://doi.org/10.1016/j.ympev.2016.05.001openalex-snapshot

On simulated annealing phase transitions in phylogeny reconstruction

inferred← citeshttps://doi.org/10.1089/cmb.2022.0197openalex-snapshot

Evaluating Compression-Based Phylogeny Estimation in the Presence of Incomplete Lineage Sorting

inferred← citeshttps://doi.org/10.1093/gbe/evz272openalex-snapshot

The Reproducibility of an Inferred Tree and the Diploidization of Gene Segregation after Genome Duplication

inferred← citeshttps://doi.org/10.1093/molbev/msaa049openalex-snapshot

Relative Efficiencies of Simple and Complex Substitution Models in Estimating Divergence Times in Phylogenomics

inferred← citeshttps://doi.org/10.1093/molbev/msab189openalex-snapshot

An Analysis of Methylome Evolution in Primates

inferred← citeshttps://doi.org/10.1093/molbev/msac043openalex-snapshot

Embracing Green Computing in Molecular Phylogenetics

inferred← citeshttps://doi.org/10.1093/molbev/msw272openalex-snapshot

The Reliability and Stability of an Inferred Phylogenetic Tree from Empirical Data

inferred← citeshttps://doi.org/10.1101/2020.02.14.949339openalex-snapshot

Relative efficiencies of simple and complex substitution models in estimating divergence times in phylogenomics

inferred← citeshttps://doi.org/10.1101/2024.02.28.582627openalex-snapshot

Testing the mettle of METAL: A comparison of phylogenomic methods using a challenging but well-resolved phylogeny

inferred← citeshttps://doi.org/10.1109/bibm49941.2020.9313237openalex-snapshot

Comparing phylogeny by compression to phylogeny by NJp and Bayesian Inference

inferred← citeshttps://doi.org/10.1109/bibm66473.2025.11356483openalex-snapshot

Scalable Alignment-Free Phylogenomics Using Normalized Compression Distance (NCD): A Case Study in Tomato (Solanum Lycopersicum) Whole Genomes

inferred← citeshttps://doi.org/10.1111/1755-0998.70163openalex-snapshot

Treeline Provides a Unified Strategy for Optimising Phylogenetic Trees Under Alternative Criteria

inferred← citeshttps://doi.org/10.1155/2021/6652445openalex-snapshot

The Chloroplastic Small Heat Shock Protein Gene KvHSP26 Is Induced by Various Abiotic Stresses in Kosteletzkya virginica

inferred← citeshttps://doi.org/10.1155/ioa/3034611openalex-snapshot

Genetic Diversity of Landrace Rice Varieties in Lower Northern Thailand Using Chloroplast DNA Markers

inferred← citeshttps://doi.org/10.11646/phytotaxa.393.3.4openalex-snapshot

Lactarius guangdongensis sp. nov. (Russulaceae, Russulales), a species of Lactarius sect. Deliciosi growing with a vulnerable five-needle pine, Pinus kwangtungensis

inferred← citeshttps://doi.org/10.1186/s12863-022-01045-xopenalex-snapshot

Developing a bioinformatics pipeline for comparative protein classification analysis

inferred← citeshttps://doi.org/10.1186/s12864-025-11304-7openalex-snapshot

Using RAD-seq to identify and differentiate the medicinal herb Scrophularia ningpoensis and its adulterants

inferred← citeshttps://doi.org/10.1186/s12906-023-04083-9openalex-snapshot

The structural characterization and bioactivity assessment of nonspecific lipid transfer protein 1 (nsLTP1) from caraway (Carum carvi) seeds

inferred← citeshttps://doi.org/10.12688/f1000research.26930.1openalex-snapshot

On the transformation of MinHash-based uncorrected distances into proper evolutionary distances for phylogenetic inference

inferred← citeshttps://doi.org/10.1371/journal.pone.0298745openalex-snapshot

Multilocus sequence typing and antibiotic resistance of Aeromonas isolated from freshwater fish in Hebei Province

inferred← citeshttps://doi.org/10.18343/jipi.30.4.689openalex-snapshot

Bioprospecting of Pectinase-Producing Bacteria from Marine Actinomycetes

inferred← citeshttps://doi.org/10.3389/fmicb.2023.1118025openalex-snapshot

Mutation-driven parallel evolution in emergence of ACE2-utilizing sarbecoviruses

inferred← citeshttps://doi.org/10.3389/fpls.2024.1492026openalex-snapshot

Genome-wide identification and expression profile of HIR gene family members in Oryza sativa L

inferred← citeshttps://doi.org/10.3390/biology15100753openalex-snapshot

The Evolution of IL6-IL6R-JAK-STAT Signaling Pathway in Metazoan

inferred← citeshttps://doi.org/10.3390/ijms21176345openalex-snapshot

Characterization of the Bacteriophage vB_EfaS-271 Infecting Enterococcus faecalis

inferred← citeshttps://doi.org/10.3390/ijms21228821openalex-snapshot

Bacteriophages vB_Sen-TO17 and vB_Sen-E22, Newly Isolated Viruses from Chicken Feces, Specific for Several Salmonella enterica Strains

inferred← citeshttps://doi.org/10.3390/life15081327openalex-snapshot

Integrated Proteomic and Molecular Identification of Thermophilic Geobacillus Strains from Algerian Desert Sands and Their Enzymatic Potential

inferred← citeshttps://doi.org/10.3390/v15051208openalex-snapshot

Virulent Phage vB_EfaS_WH1 Removes Enterococcus faecalis Biofilm and Inhibits Its Growth on the Surface of Chicken Meat

inferred← citeshttps://doi.org/10.46912/jbrcp.221openalex-snapshot

Cryptococcal Meningitis amomg HIV-Infected and HIV-Uninfected Patients in Jos, North Central Nigeria

inferred← citeshttps://doi.org/10.48550/arxiv.1612.01602openalex-snapshot

Species tree estimation using Neighbor Joining

inferred← citeshttps://doi.org/10.48550/arxiv.1708.02626openalex-snapshot

A combinatorial method for connecting BHV spaces representing different numbers of taxa

inferred← citeshttps://doi.org/10.6084/m9.figshare.20012907openalex-snapshot

Additional file 12 of Developing a bioinformatics pipeline for comparative protein classification analysis

inferred← citeshttps://doi.org/10.6084/m9.figshare.20012934openalex-snapshot

Additional file 1 of Developing a bioinformatics pipeline for comparative protein classification analysis

inferred← citeshttps://doi.org/10.6084/m9.figshare.26605354openalex-snapshot

Additional file 1 of The structural characterization and bioactivity assessment of nonspecific lipid transfer protein 1 (nsLTP1) from caraway (Carum carvi) seeds

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.