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

Mechanistic Models: Compartment Models in Algorithms for Numerical Problem Solving01:29

Mechanistic Models: Compartment Models in Algorithms for Numerical Problem Solving

Mechanistic models play a crucial role in algorithms for numerical problem-solving, particularly in nonlinear mixed effects modeling (NMEM). These models aim to minimize specific objective functions by evaluating various parameter estimates, leading to the development of systematic algorithms. In some cases, linearization techniques approximate the model using linear equations.
In individual population analyses, different algorithms are employed, such as Cauchy's method, which uses a...
Methods of Medium Optimization01:28

Methods of Medium Optimization

Optimizing growth media enhances microbial proliferation and maximizes product yield. Statistical experimental design methodologies provide structured and reproducible approaches, offering progressively higher levels of robustness and efficiency.The One-Factor-at-a-Time (OFAT) MethodThe One-Factor-at-a-Time (OFAT) method involves adjusting a single variable while keeping all others constant. However, it cannot detect interactions between variables, often leading to suboptimal outcomes when...
Evaluating Limits by Direct Substitution01:29

Evaluating Limits by Direct Substitution

In the analysis of functions that represent continuous physical phenomena, it is often necessary to determine the output value as the input approaches a specific point. When a combination of algebraic terms defines the function and exhibits no discontinuities or abrupt changes near the point of interest, the limit of the function can be evaluated directly. This process, known as direct substitution, involves replacing the variable in the expression with the value it approaches.Direct...
Predicting Products: Substitution vs. Elimination02:52

Predicting Products: Substitution vs. Elimination

When a nucleophile and an alkyl halide react, nucleophilic substitution and β-elimination reactions compete to generate products.
The following factors can influence the mechanisms competing against each other:
State Function, Exact and Inexact Differentials01:27

State Function, Exact and Inexact Differentials

A state function is a thermodynamic property that depends solely on the current state of a system, irrespective of its history or how it arrived at that state. These functions are represented by capital letters, such as U, H, and S, which stand for internal energy, enthalpy, and entropy, respectively.For instance, the value of internal energy depends on the system's state variables and remains unaffected by the process path. This means that whether the system underwent a linear process or a...
Rationalizing Substitutions01:29

Rationalizing Substitutions

Integrals involving non-rational functions are often difficult to evaluate using standard techniques, especially when radicals appear in the integrand. Rationalizing substitution provides a systematic method for simplifying such integrals by converting them into rational forms that are easier to handle.Consider a rod whose linear mass density depends on a constant linear density, a characteristic length, and the distance from the left end of the rod. Determining the total mass requires...

You might also read

Related Articles

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

Sort by
Same author

Targeted Chromosomal Sequencing of Wild Bonobos Identifies a Genetically Distinct Subpopulation East of the Lomami River.

bioRxiv : the preprint server for biology·2026
Same author

Accessible, Realistic Genome Simulation with Selection Using stdpopsim.

Molecular biology and evolution·2025
Same author

Punic people were genetically diverse with almost no Levantine ancestors.

Nature·2025
Same author

Accessible, realistic genome simulation with selection using stdpopsim.

bioRxiv : the preprint server for biology·2025
Same author

Deep genetic substructure within bonobos.

Current biology : CB·2024
Same author

Accurate prediction of disease-risk factors from volumetric medical scans by a deep vision model pre-trained with 2D scans.

Nature biomedical engineering·2024

Related Experiment Video

Updated: Jun 22, 2026

A Psychophysics Paradigm for the Collection and Analysis of Similarity Judgments
08:12

A Psychophysics Paradigm for the Collection and Analysis of Similarity Judgments

Published on: March 1, 2022

Towards optimal distance functions for stochastic substitution models.

Ilan Gronau1, Shlomo Moran, Irad Yavneh

  • 1Technion, Computer Science, Taub Building, Technion City, 32000 Haifa, Israel. ilangr@cs.technion.ac.il

Journal of Theoretical Biology
|June 9, 2009
PubMed
Summary

Selecting appropriate distance functions significantly improves phylogenetic tree accuracy. This study introduces a framework and method for choosing optimal distances in evolutionary sequence analysis, enhancing tree reconstruction precision.

Related Experiment Videos

Last Updated: Jun 22, 2026

A Psychophysics Paradigm for the Collection and Analysis of Similarity Judgments
08:12

A Psychophysics Paradigm for the Collection and Analysis of Similarity Judgments

Published on: March 1, 2022

Area of Science:

  • Computational Biology
  • Evolutionary Biology
  • Bioinformatics

Background:

  • Phylogenetic tree reconstruction relies on accurate inter-species distance estimation.
  • Current methods often use a single, fixed distance function, potentially limiting accuracy.

Purpose of the Study:

  • To characterize valid distance functions for stochastic evolutionary models.
  • To develop a method for selecting optimal distance functions to improve phylogenetic tree accuracy.

Main Methods:

  • Developed a general framework for constructing families of additive distance functions.
  • Proposed a method for selecting (near) optimal distance functions.
  • Utilized simulation results to support theoretical analysis.

Main Results:

  • Characterized the family of valid distance functions for specific substitution models.
  • Demonstrated that deliberate selection of distance functions significantly enhances distance estimates.
  • Showcased improved accuracy in reconstructed phylogenetic trees due to optimized distance selection.

Conclusions:

  • The choice of distance function is critical for accurate phylogenetic inference.
  • The proposed framework and selection method offer a significant advancement in distance-based tree reconstruction.
  • Optimizing distance functions leads to more reliable evolutionary trees.