PhyGraFT: a network-based method for phylogenetic trait analysis

With the determination of numerous viral and bacterial genome sequences, phylogeny-trait associations are now being studied. In these studies, phylogenetic trees were first reconstructed, and trait data were analyzed based on the reconstructed tree. However, in some cases, such as fast evolution sequences and gene-sharing network data, reconstructing the phylogenetic tree is challenging. In such cases, network-thinking, instead of tree-thinking, is gaining attention. Here, we propose a novel network-thinking approach, PhyGraFT, to analyze trait data from the network. We validated that PhyGraFT can find phylogenetic signals and associations of traits with the simulation dataset. We applied PhyGraFT for influenza type A and virome gene-sharing datasets. As a result, we identified several evolutionary structures and their associated traits. Our approach is expected to provide novel insights into network-thinking not only for typical phylogenetics but also for various biological data, such as antibody evolution.

• Publication year

  2022

• Venue

  bioRxiv

• Publication date

  2022-05-30

• Fields of study

  Biology, Computer Science

• Identifiers
  DOI 10.1101/2022.05.29.493939
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar

• No claims are published for this paper.

• No concepts are published for this paper.

• Whole-genome sequencing and gene sharing network analysis powered by machine learning identifies antibiotic resistance sharing between animals, humans and environment in livestock farming

  2022cited by this paper
• Quantifying the effect of experimental perturbations at single-cell resolution

  2021cited by this paper
• Graph Splitting: A Graph-Based Approach for Superfamily-scale Phylogenetic Tree Reconstruction.

  2019cited by this paper
• A non-parametric analytic framework for within-host viral phylogenies and a test for HIV-1 founder multiplicity

  2019cited by this paper
• A Comprehensive Survey on Graph Neural Networks

  2019cited by this paper
• Large-scale network analysis reveals the sequence space architecture of antibody repertoires

  2019cited by this paper
• Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks

  2019cited by this paper
• Characterizing and comparing phylogenetic trait data from their normalized Laplacian spectrum

  2019cited by this paper
• The phylogenomics of evolving virus virulence

  2018cited by this paper
• Graph Spectral Image Processing

  2018influential reference
• Graph Neural Networks: A Review of Methods and Applications

  2018cited by this paper
• MMseqs2: sensitive protein sequence searching for the analysis of massive data sets

  2017cited by this paper
• Network-Thinking: Graphs to Analyze Microbial Complexity and Evolution

  2016cited by this paper
• Graph Laplacian Regularization for Image Denoising: Analysis in the Continuous Domain

  2016cited by this paper
• phylosignal: an R package to measure, test, and explore the phylogenetic signal

  2016cited by this paper
• Characterizing and comparing phylogenies from their Laplacian spectrum

  2015cited by this paper
• Microbiomes in light of traits: A phylogenetic perspective

  2015cited by this paper
• Consequences of domain insertion on sequence-structure divergence in a superfold

  2013cited by this paper
• Viral Phylodynamics

  2013cited by this paper
• MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

  2013cited by this paper
• How to measure and test phylogenetic signal

  2012cited by this paper
• CD-HIT: accelerated for clustering the next-generation sequencing data

  2012cited by this paper
• The emerging field of signal processing on graphs: Extending high-dimensional data analysis to networks and other irregular domains

  2012cited by this paper
• Evolutionary analysis of the dynamics of viral infectious disease

  2009cited by this paper
• INDELible: A Flexible Simulator of Biological Sequence Evolution

  2009cited by this paper
• Modular networks and cumulative impact of lateral transfer in prokaryote genome evolution

  2008cited by this paper
• Correlating viral phenotypes with phylogeny: accounting for phylogenetic uncertainty.

  2008cited by this paper
• Estimating a binary character's effect on speciation and extinction.

  2007cited by this paper
• Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences

  2006cited by this paper
• Consensus proposals for a unified system of nomenclature of hepatitis C virus genotypes

  2005cited by this paper
• Phylodynamic Analysis of Human Immunodeficiency Virus Type 1 in Distinct Brain Compartments Provides a Model for the Neuropathogenesis of AIDS

  2005cited by this paper
• Compartmentalization of Human Immunodeficiency Virus Type 1 between Blood Monocytes and CD4+ T Cells during Infection

  2004cited by this paper
• Laplacian Eigenmaps for Dimensionality Reduction and Data Representation

  2003cited by this paper
• A method for testing the assumption of phylogenetic independence in comparative data

  1999cited by this paper
• A cladistic measure of gene flow inferred from the phylogenies of alleles.

  1989cited by this paper
• The neighbor-joining method: a new method for reconstructing phylogenetic trees.

  1987cited by this paper
• Edinburgh Research Explorer Identification of shared populations of human immunodeficiency virus type 1 infecting microglia and tissue macrophages outside the central nervous system

  year unknowncited by this paper

• No citing papers are available for this paper.