Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Experiment Videos

primetv: a viewer for reconciled trees.

Bengt Sennblad1, Eva Schreil, Ann-Charlotte Berglund Sonnhammer

  • 1Stockholm Bioinformatics Center and Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden. bengt.sennblad@sbc.su.se <bengt.sennblad@sbc.su.se>

BMC Bioinformatics
|May 9, 2007
PubMed
Summary
This summary is machine-generated.

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Computational pathology annotation enhances the resolution and interpretation of breast cancer spatial transcriptomics data.

NPJ precision oncology·2025
Same author

Exonize: a tool for finding and classifying exon duplications in annotated genomes.

Bioinformatics advances·2025
Same author

Genome sequences of six clinical isolates of <i>Candida parapsilosis</i> exhibiting different degrees and temporal regulation of biofilm formation.

Microbiology resource announcements·2025
Same author

Author Correction: Integrative spatial and genomic analysis of tumor heterogeneity with Tumoroscope.

Nature communications·2025
Same author

Sparse Neighbor Joining: rapid phylogenetic inference using a sparse distance matrix.

Bioinformatics (Oxford, England)·2024
Same author

CopyMix: Mixture model based single-cell clustering and copy number profiling using variational inference.

Computational biology and chemistry·2024
Same journal

Research on multi-trait genome association study method based on Shannon information entropy.

BMC bioinformatics·2026
Same journal

A multi-view feature fusion framework with interpretable graph convolution for predicting microbe-drug associations.

BMC bioinformatics·2026
Same journal

Covariance decomposition for distance based species tree estimation.

BMC bioinformatics·2026
Same journal

SNPio: a Python interface for population genomic data processing.

BMC bioinformatics·2026
Same journal

SpaHNR: a spatial domain identification method via sparse attention-based hierarchical node representation and multi-view contrastive learning.

BMC bioinformatics·2026
Same journal

OpenIMC: an open-source platform for analyzing single-cell and spatial proteomics by imaging mass cytometry.

BMC bioinformatics·2026
See all related articles

PrimeTV is a new tool that automatically visualizes general tree reconciliations, aiding in understanding evolutionary processes like gene family evolution. This software simplifies the creation of complex tree-within-tree illustrations for scientific and educational purposes.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Evolutionary Biology

Background:

  • Evolutionary processes can be modeled as trees evolving within other trees, a concept known as tree reconciliation.
  • Visualizing these reconciliations is crucial for understanding phenomena like gene family evolution and parasite-host co-speciation.
  • Current tools are limited to the most parsimonious reconciliations, excluding many biologically relevant scenarios.

Purpose of the Study:

  • To develop a novel software tool for visualizing general tree reconciliations, including non-parsimonious ones.
  • To provide an automated solution for generating tree-within-tree illustrations.
  • To facilitate the communication and understanding of complex evolutionary relationships.

Main Methods:

  • Development of a new reconciliation viewer named primetv.

Related Experiment Videos

  • Implementation of primetv to read reconciled trees in an extended Newick format.
  • Creation of helper programs (readReconciliation, reconcile) to aid input construction.
  • Inclusion of a web service for user-friendly access.

    • Main Results:

    • PrimeTV is the first automatic tool for illustrating general tree reconciliations.
    • The software generates tree-within-tree illustrations with adjustable output attributes (color, layout).
    • Helper programs and a web service enhance usability for both developers and casual users.

    Conclusions:

    • PrimeTV enables easy production of general reconciliation illustrations, clarifying evolutionary impacts.
    • The tool enhances scientific presentations and educational materials.
    • PrimeTV is available as a standalone tool and web service under the GNU GPL.