ArticlePLoS computational biology2020
AncesTree: An interactive immunoglobulin lineage tree visualizer.
Article in PLoS computational biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Pan-neutralization of parainfluenza viruses by a hemagglutinin-neuraminidase antibody.bioRxiv : the preprint server for biology · 2026Article
- Article
- Discovery, recognized antigenic structures, and evolution of cross-serotype broadly neutralizing antibodies from porcine B-cell repertoires against foot-and-mouth disease virus.PLoS pathogens · 2024Article
- RAIN: machine learning-based identification for HIV-1 bNAbs.Nature communications · 2024Article
- RAIN: a Machine Learning-based identification for HIV-1 bNAbs.Research square · 2024Article
- Streamlined Multi-Attribute Assessment of an Array of Clinical-Stage Antibodies: Relationship Between Degradation and Stability.Applied spectroscopy · 2024Article
- B cell phylogenetics in the single cell era.Trends in immunology · 2024Review
- Article
- ViCloD, an interactive web tool for visualizing B cell repertoires and analyzing intraclonal diversities: application to human B-cell tumors.NAR genomics and bioinformatics · 2023Article
- Lineage Reconstruction of In Vitro Identified Antigen-Specific Autoreactive B Cells from Adaptive Immune Receptor Repertoires.International journal of molecular sciences · 2022Article
- Article
- IgIDivA: immunoglobulin intraclonal diversification analysis.Briefings in bioinformatics · 2022Article
- AIRRscape: An interactive tool for exploring B-cell receptor repertoires and antibody responses.PLoS computational biology · 2022Article
- Antibodies to combat viral infections: development strategies and progress.Nature reviews. Drug discovery · 2022Review
- Broad betacoronavirus neutralization by a stem helix-specific human antibody.Science (New York, N.Y.) · 2021Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
High-throughput sequencing of human immunoglobulin genes allows analysis of antibody repertoires and the reconstruction of clonal lineage evolution. The study of antibodies (Abs) affinity maturation is of specific interest to understand the generation of Abs with high affinity or broadly neutralizing activities. Moreover, phylogenic analysis enables the identification of the key somatic mutations required to achieve optimal antigen binding. The Immcantation framework provides a start-to-finish set of analytical methods for high-throughput adaptive immune receptor repertoire sequencing (AIRR-Seq; Rep-Seq) data. Furthermore, Immcantation's Change-O package has developed IgPhyML, an algorithm designed to build specifically immunoglobulin (Ig) phylogenic trees. Meanwhile Phylip, an algorithm that has been originally developed for applications in ecology and macroevolution, can also be used for the phylogenic reconstruction of antibodies maturation pathway. To complement Ig lineages made by IgPhyML or Dnaml (Phylip), we developed AncesTree, a graphic user interface (GUI) that aims to give researchers the opportunity to interactively explore antibodies clonal evolution. AncesTree displays interactive immunoglobulins phylogenic tree, Ig related mutations and sequence alignments using additional information coming from specialized antibody tools. The GUI is a Java standalone application allowing interaction with Ig tree that can run under Windows, Linux and Mac OS.
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Registered trials
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