Article

Covary: A translation-aware framework for alignment-free phylogenetics using machine learning

2025-11-14

Abstract excerpt

<h4>ABSTRACT</h4> In large-scale phylogenetic analysis, incorporating translation awareness is critical to account for the genotypic and phenotypic dimensions underlying biological diversification. Covary is a machine learning-based framework that analyzes, clusters, and compares genetic sequences through alignment-free, translation-aware embeddings. By integrating codon-boundary and intra-sequence positional inf...

Topics

Open a Topic to create a Post that cites this publication.

Identifiers and source

Literature Corpus work: 0fa5a246-a372-5e24-82d9-e62aaac13173
DOI: 10.1101/2025.11.13.687960

Open publication

Related research

Semantic proximity does not establish scientific evidence.

Click a neighbor to travelStep 1 · 12 closest

Covary: A translation-aware framework for alignment-free phylogenetics using machine learningDOI 10.1101/2025.11.13.687960Read

A Daily-Updated Database and Tools for Comprehensive SARS-CoV-2 Mutation-Annotated Trees.Semantic proximity Read

Single-nucleotide conservation state annotation of the SARS-CoV-2 genome.Semantic proximity Read

matOptimize: a parallel tree optimization method enables online phylogenetics for SARS-CoV-2Semantic proximity Read

Robust expansion of phylogeny for fast-growing genome sequence dataSemantic proximity Read

Compressive pangenomics using mutation-annotated networks.Semantic proximity Read

A novel Vector-Symbolic Architecture for graph encoding and its application to viral pangenome-based species classificationSemantic proximity Read

Integrating Fréchet distance and AI reveals the evolutionary trajectory and origin of SARS‐CoV‐2Semantic proximity Read

Embeddings from protein language models predict conservation and variant effectsSemantic proximity Read

bronko: ultrafast, alignment-free detection of viral genome variationSemantic proximity Read

Illuminating the Virosphere’s Dark Matter using Hierarchical Deep LearningSemantic proximity Read

MGtree: A Fast and Flexible Alignment-Based Metagenomics Pipeline.Semantic proximity Read

Preparing For the Next Pandemic: Learning Wild Mutational Patterns At Scale For Analyzing Sequence Divergence In Novel PathogensSemantic proximity Read