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 Concept Videos

Survival Tree01:19

Survival Tree

86
Survival trees are a non-parametric method used in survival analysis to model the relationship between a set of covariates and the time until an event of interest occurs, often referred to as the "time-to-event" or "survival time." This method is particularly useful when dealing with censored data, where the event has not occurred for some individuals by the end of the study period, or when the exact time of the event is unknown.
 Building a Survival Tree
Constructing a...
86
Phylogenetic Trees03:21

Phylogenetic Trees

45.3K
Phylogenetic trees come in many forms. It matters in which sequence the organisms are arranged from the bottom to the top of the tree, but the branches can rotate at their nodes without altering the information. The lines connecting individual nodes can be straight, angled, or even curved.
45.3K

You might also read

Related Articles

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

Sort by
Same author

Bridging quantum noise and classical electrodynamics with stochastic methods.

Nature communications·2026
Same author

Vibrationally Induced Resonances in Lasing.

The journal of physical chemistry letters·2026
Same author

Prostate ageing across the adult lifespan: population MRI evidence from 30 000 men.

Age and ageing·2026
Same author

Catch-Up Weight Gain and Gut Microbiota Development in Full-Term Small for Gestational Age Children During the First Year of Life-A Prospective Cohort Study.

American journal of human biology : the official journal of the Human Biology Council·2026
Same author

Coexistence of weak and strong coupling in a photonic molecule through dissipative coupling to a quantum dot.

Nanophotonics (Berlin, Germany)·2025
Same author

Toward Single-Photon Detection with Superconducting Niobium Diselenide Nanowires.

ACS photonics·2025

Related Experiment Video

Updated: Jul 4, 2025

A Practical Guide to Phylogenetics for Nonexperts
12:00

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

35.4K

NewickTreeModifier: A simple web tool to prune and modify Newick trees.

Lynn Ogoniak1, Raphael Steffen1, Norbert Grundmann2

  • 1Institute of Experimental Pathology, ZMBE, University of Münster, Münster, Germany.

The Journal of Heredity
|February 2, 2024
PubMed
Summary
This summary is machine-generated.

NewickTreeModifier (NTM) simplifies phylogenetic tree manipulation for large-scale sequence analyses. This web tool trims and modifies Newick trees, enabling efficient selection of species for evolutionary studies.

Keywords:
NTM web interfaceNewick treemodify phylogenetic treespruning phylogenetic trees

More Related Videos

The ITS2 Database
16:17

The ITS2 Database

Published on: March 12, 2012

30.8K
Author Spotlight: Investigating the Role of Repetitive DNA Misregulation in Cancer Initiation and Immunotherapy Resistance
04:58

Author Spotlight: Investigating the Role of Repetitive DNA Misregulation in Cancer Initiation and Immunotherapy Resistance

Published on: December 13, 2024

2.4K

Related Experiment Videos

Last Updated: Jul 4, 2025

A Practical Guide to Phylogenetics for Nonexperts
12:00

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

35.4K
The ITS2 Database
16:17

The ITS2 Database

Published on: March 12, 2012

30.8K
Author Spotlight: Investigating the Role of Repetitive DNA Misregulation in Cancer Initiation and Immunotherapy Resistance
04:58

Author Spotlight: Investigating the Role of Repetitive DNA Misregulation in Cancer Initiation and Immunotherapy Resistance

Published on: December 13, 2024

2.4K

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Evolutionary Biology

Background:

  • Phylogenetic tree reconstruction and large-scale selection analyses necessitate trees in Newick format.
  • Existing tools may lack flexibility for specific species subsetting and format conversion.

Purpose of the Study:

  • To develop a user-friendly web-based tool for modifying Newick trees.
  • To facilitate the selection and pruning of species for phylogenetic analyses.

Main Methods:

  • Developed NewickTreeModifier (NTM), a web tool for Newick tree manipulation.
  • Integrated internal converters for FASTA, NEXUS, and PHYLIP formats.
  • Provided options for species selection via lists, checklists, or master trees.

Main Results:

  • NTM allows users to prune trees to selected species efficiently.
  • Supports plant, insect, and vertebrate master trees with extensive species coverage.
  • Outputs modified trees in Newick format suitable for downstream analyses.

Conclusions:

  • NTM offers a streamlined approach to preparing phylogenetic trees for large-scale analyses.
  • The tool enhances accessibility and efficiency in evolutionary biology research.