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

Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

5.7K
Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
5.7K
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
Phylogeny01:23

Phylogeny

43.8K
Phylogeny is concerned with the evolutionary diversification of organisms or groups of organisms. A group of organisms with a name is called a taxon (singular). Taxa (plural) can span different levels of the evolutionary hierarchy. For instance, the group containing all birds is a taxon (comprising the class Aves), and the group of all species of daisies (the genus Bellis) is a taxon. Phylogenies can likewise include just one genus (i.e., depict species relationships) or span an entire kingdom.
43.8K

You might also read

Related Articles

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

Sort by
Same author

PTMs_Closed_Search: Multiple Post-Translational Modification Closed Search Using Reduced Search Space and Transferred FDR.

Proteomes·2026
Same author

Inferring binding specificities of human transcription factors with the wisdom of crowds.

bioRxiv : the preprint server for biology·2025
Same author

Cross-platform motif discovery and benchmarking to explore binding specificities of poorly studied human transcription factors.

Communications biology·2025
Same author

GAME: Genomic API for Model Evaluation.

bioRxiv : the preprint server for biology·2025
Same author

Rare Evolutionary Events Support the Phylogenetic Placement of Orthonectida Within Annelida.

International journal of molecular sciences·2025
Same author

Restriction-Modification Systems Specific toward GGATC, GATGC, and GATGG. Part 1. Evolution and Ecology.

Biochemistry. Biokhimiia·2025

Related Experiment Video

Updated: Jun 24, 2025

A Practical Guide to Phylogenetics for Nonexperts
12:00

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

35.3K

PhyloBench: A Benchmark for Evaluating Phylogenetic Programs.

Sergey Spirin1,2, Andrey Sigorskikh3, Aleksei Efremov3

  • 1Belozersky Institute, Lomonosov Moscow State University, Moscow, Russia.

Molecular Biology and Evolution
|June 11, 2024
PubMed
Summary

PhyloBench provides a benchmark for comparing phylogenetic inference programs using real protein sequences. Distance methods, particularly Balanced Minimum Evolution, demonstrated superior accuracy over maximum likelihood and maximum parsimony.

Keywords:
benchmarkphylogenetic inference

More Related Videos

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
08:57

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

15.9K
Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group
07:49

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group

Published on: August 16, 2017

7.1K

Related Experiment Videos

Last Updated: Jun 24, 2025

A Practical Guide to Phylogenetics for Nonexperts
12:00

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

35.3K
Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
08:57

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

15.9K
Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group
07:49

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group

Published on: August 16, 2017

7.1K

Area of Science:

  • * Computational Biology
  • * Evolutionary Biology
  • * Bioinformatics

Background:

  • * Phylogenetic inference from protein sequences is crucial but complex due to numerous algorithms and parameters.
  • * A lack of standardized benchmarks for real protein sequences hindered objective program comparison.
  • * Evaluating phylogenetic methods requires robust metrics and datasets for accurate assessment.

Purpose of the Study:

  • * To develop and introduce PhyloBench, a novel benchmark for assessing phylogenetic inference quality.
  • * To evaluate the performance of popular phylogenetic programs using natural protein sequences.
  • * To identify the most accurate phylogenetic methods for protein sequence data.

Main Methods:

  • * PhyloBench utilizes natural protein sequences from orthologous evolutionary domains, not simulated data.
  • * Tree accuracy is measured by the distance to the reference species tree, with Robinson-Foulds distance proving most reliable.
  • * Performance of various phylogenetic algorithms, including distance, maximum likelihood, maximum parsimony, and Bayesian methods, was assessed.

Main Results:

  • * Distance-based phylogenetic methods outperformed maximum likelihood and maximum parsimony on natural protein sequences.
  • * The Balanced Minimum Evolution method, implemented in FastME, yielded the most accurate results among tested methods.
  • * The Bayesian program MrBayes performed better than maximum likelihood but was less accurate than distance methods.

Conclusions:

  • * PhyloBench offers a valuable resource for the scientific community to evaluate phylogenetic inference tools.
  • * Distance methods represent a more accurate approach for phylogenetic reconstruction from protein sequences compared to ML and MP.
  • * The Balanced Minimum Evolution method is recommended for high-accuracy phylogenetic analysis of protein data.