ReviewBioengineering (Basel, Switzerland)2024
Common Methods for Phylogenetic Tree Construction and Their Implementation in R.
Review in Bioengineering (Basel, Switzerland), 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
34 citing papers in PubMed.
- Unveiling the terra cognita of sequence spaces using Cartesian projection of asymmetric distances.NAR genomics and bioinformatics · 2026Article
- An Overview of Epidemiological Tools That Support the Progress of Foot-and-Mouth Disease Control in Southeast Asia.Pathogens (Basel, Switzerland) · 2026Review
- Identification of PepperPlants (Basel, Switzerland) · 2026Article
- Integrative immunoinformatics and structural modeling for the rational design of a multi-epitope vaccine candidate against human cytomegalovirus.Scientific reports · 2026Article
- seqLens: Optimizing Language Models for Genomic Predictions.Molecular biology and evolution · 2026Article
- Treeline Provides a Unified Strategy for Optimising Phylogenetic Trees Under Alternative Criteria.Molecular ecology resources · 2026Article
- High genetic diversity of porcine rotavirus A, B, and C in Hungary with putative novel VP4 genotypes.BMC veterinary research · 2026Article
- Biosynthesis of antibacterial zinc oxide nanoparticles from endophytic Streptomyces werraensis.Scientific reports · 2026Article
- phyloPipeR: An R Package for End-to-End Phylogenetic Reconstruction and Tree Comparison.Current issues in molecular biology · 2026Article
- Polyphasic Characterization of Acetobacter indonesiensis UNPADCC 01-5 Isolated From a Traditional Fermented Food, Oncom Merah.Environmental microbiology reports · 2026Article
- Concatenation, Conflict, and Complexity: Genealogical Heterogeneity Mimics Substitutional Heterogeneity for Nucleotide Model Selection.Journal of molecular evolution · 2026Article
- Genome-wide analysis of the NAC gene family in Qu-1 doubled haploid cell line from Populus simonii × P. nigra and expression patterns under abscisic acid (ABA) treatment.BMC plant biology · 2026Article
- BAT: an integrated pipeline for gene tree construction, annotation, and functional inference.bioRxiv : the preprint server for biology · 2026Article
- Establishment of a matrix-assisted laser desorption/ionization time-of-flight mass spectrometry database and evaluation of different methods for cluster analysis of marine bacteria.Journal of medical microbiology · 2026Article
- Article
- Integrative Inference of Spatially Resolved Cell Lineage Trees using LineageMap.bioRxiv : the preprint server for biology · 2026Article
- Interrelational Proteomic Sequence Features Enhance Predictive Modeling: Application to COVID-19 Severity.Biomedicines · 2026Article
- Genetic diversity and population structure of pearl millet in the Senegalese germplasm.PloS one · 2026Article
- Apicomplexan parasites in urban corvids: Presence ofCurrent research in parasitology & vector-borne diseases · 2026Article
- Studying the Evolution of Protein Structure One Superfamily at a Time.Methods in molecular biology (Clifton, N.J.) · 2026Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors.
Funding
Abstract
A phylogenetic tree can reflect the evolutionary relationships between species or gene families, and they play a critical role in modern biological research. In this review, we summarize common methods for constructing phylogenetic trees, including distance methods, maximum parsimony, maximum likelihood, Bayesian inference, and tree-integration methods (supermatrix and supertree). Here we discuss the advantages, shortcomings, and applications of each method and offer relevant codes to construct phylogenetic trees from molecular data using packages and algorithms in R. This review aims to provide comprehensive guidance and reference for researchers seeking to construct phylogenetic trees while also promoting further development and innovation in this field. By offering a clear and concise overview of the different methods available, we hope to enable researchers to select the most appropriate approach for their specific research questions and datasets.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.