ArticleiMeta2023
Using PhyloSuite for molecular phylogeny and tree-based analyses.
Article in iMeta, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 341 papers.
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Who cites it
341 citing papers in PubMed.
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- Complete Mitochondrial Genome of Turrum coeruleopinnatum Provides Phylogenetic Context and Candidate Selection Signals Within Carangidae.Biochemical genetics · 2026Article
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- Calpains as Potential Regulators of Microtubule-Associated Cytokinesis: A Cross-Eukaryotic Unifying Hypothesis.Life (Basel, Switzerland) · 2026Article
- Complete Chloroplast Genome ofEcology and evolution · 2026Article
- Morphology, Chemistry, and Phylogeny Reveal Two New Species of the GenusJournal of fungi (Basel, Switzerland) · 2026Article
- Comparative mitogenomic study of the brown accentor (Prunella fulvescens) and a sympatric relative across an altitudinal gradient.Scientific reports · 2026Article
- Characterization of an Endophytic Fusarium odoratissimum Strain 25Current microbiology · 2026Article
- Complete mitochondrial genome ofMicrobiology resource announcements · 2026Article
- Complete mitochondrial genome ofMicrobiology resource announcements · 2026Article
281 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Phylogenetic analysis has entered the genomics (multilocus) era. For less experienced researchers, conquering the large number of software programs required for a multilocus-based phylogenetic reconstruction can be somewhat daunting and time-consuming. PhyloSuite, a software with a user-friendly GUI, was designed to make this process more accessible by integrating multiple software programs needed for multilocus and single-gene phylogenies and further streamlining the whole process. In this protocol, we aim to explain how to conduct each step of the phylogenetic pipeline and tree-based analyses in PhyloSuite. We also present a new version of PhyloSuite (v1.2.3), wherein we fixed some bugs, made some optimizations, and introduced some new functions, including a number of tree-based analyses, such as signal-to-noise calculation, saturation analysis, spurious species identification, and etc. The step-by-step protocol includes background information (i.e., what the step does), reasons (i.e., why do the step), and operations (i.e., how to do it). This protocol will help researchers quick-start their way through the multilocus phylogenetic analysis, especially those interested in conducting organelle-based analyses.
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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.