Article

Robust expansion of phylogeny for fast-growing genome sequence data

2022-01-03

Abstract excerpt

Massive sequencing of SARS-CoV-2 genomes has led to a great demand for adding new samples to a reference phylogeny instead of building the tree from scratch. To address such challenge, we proposed an algorithm ‘TIPars’ by integrating parsimony analysis with pre-computed ancestral sequences. Compared to four state-of-the-art methods on four benchmark datasets (SARS-CoV-2, Influenza virus, Newcastle disease virus an...

Topics

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

Identifiers and source

Literature Corpus work: 50ae59d8-7647-59a3-9eee-ee2ea754ce39
DOI: 10.1101/2021.12.30.474610

Open publication

Related research

Semantic proximity does not establish scientific evidence.

Click a neighbor to travelStep 1 · 12 closest

Robust expansion of phylogeny for fast-growing genome sequence dataDOI 10.1101/2021.12.30.474610Read

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

DecentTree: Scalable Neighbour-Joining for the Genomic EraSemantic proximity Read

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

Covary: A translation-aware framework for alignment-free phylogenetics using machine learningSemantic proximity Read

TopHap: rapid inference of key phylogenetic structures from common haplotypes in large genome collections with limited diversity.Semantic proximity Read

Scalable Reconstruction of SARS-CoV-2 Phylogeny with Recurrent Mutations.Semantic proximity Read

Topological data analysis identifies emerging adaptive mutations in SARS-CoV-2Semantic proximity Read

Phylogenetic Analysis of SARS-CoV-2 Data Is Difficult.Semantic proximity Read

Ultrafast Sample placement on Existing tRees (UShER) enables real-time phylogenetics for the SARS-CoV-2 pandemic.Semantic proximity Read

Ultrafast Sample Placement on Existing Trees (UShER) Empowers Real-Time Phylogenetics for the SARS-CoV-2 PandemicSemantic proximity Read

Analysis SARS-CoV-2 Genomes of G20 Areas on Phylogeny Tree, t-SNE based on Machine LearningSemantic proximity Read

Efficient comparative phylogenetics on large trees.Semantic proximity Read