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

Phylogeny01:23

Phylogeny

56.4K
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.
56.4K
Phylogenetic Trees03:21

Phylogenetic Trees

49.0K
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.
49.0K
Modern Molecular Taxonomy01:29

Modern Molecular Taxonomy

467
Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...
467
Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

6.7K
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...
6.7K
Gene Evolution - Fast or Slow?02:05

Gene Evolution - Fast or Slow?

7.8K
The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
In contrast, regions which code...
7.8K
Synteny and Evolution02:31

Synteny and Evolution

3.6K
John H. Renwick first coined the term “synteny” in 1971, which refers to the genes present on the same chromosomes, even if they are not genetically linked. The species with common ancestry tend to show conserved syntenic regions. Therefore, the concept of synteny is nowadays used to describe the evolutionary relationship between species.
Around 80 million years ago, the human and mice lineages diverged from the common ancestor. During the course of evolution, the ancestral...
3.6K

You might also read

Related Articles

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

Sort by
Same author

A deep learning model for automated identification of age-related macular degeneration atrophy.

Graefe's archive for clinical and experimental ophthalmology = Albrecht von Graefes Archiv fur klinische und experimentelle Ophthalmologie·2026
Same author

One Size Might Not Fit All: A Tailored Approach to Psychological Intergroup Interventions.

Personality & social psychology bulletin·2026
Same author

Broken Promises: Betrayal and Support for Violence in Intergroup Relations.

Personality & social psychology bulletin·2026
Same author

A novel momentum-based intervention sustains real-life participation in a social movement.

Scientific reports·2026
Same author

The disappointing (not hateful) divide: uncovering the negative emotions at the heart of affective polarization.

Cognition & emotion·2026
Same author

A global Youth Peacebuilding Beliefs Scale.

Communications psychology·2026
Same journal

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

BMC bioinformatics·2026
Same journal

NAP: an open source pipeline for cross-domain microbiome profiling using Nanopore sequencing-derived amplicon data.

BMC bioinformatics·2026
Same journal

SurvGME: an R package for survival analysis with graphical and measurement error models.

BMC bioinformatics·2026
Same journal

SimMapNet: a Bayesian framework for gene regulatory network inference using gene ontology similarities as external hint.

BMC bioinformatics·2026
Same journal

Dual channel drug-drug interactions extraction based on cross attention.

BMC bioinformatics·2026
Same journal

FeSseqdb: a curated sequence-level database and interpretable machine learning framework for identifying iron-sulfur proteins.

BMC bioinformatics·2026
See all related articles

Related Experiment Videos

Haplotype reconstruction using perfect phylogeny and sequence data.

Anatoly Efros1, Eran Halperin

  • 1The Blavatnik School of Computer Science, Tel-Aviv University, Tel-Aviv, Israel. talefros@gmail.com

BMC Bioinformatics
|April 28, 2012
PubMed
Summary
This summary is machine-generated.

This study introduces Perfect Phylogeny Haplotypes from Sequencing (PPHS), a new algorithm for haplotype phasing using high-throughput sequencing data. PPHS improves accuracy in low-coverage and high-error scenarios.

Related Experiment Videos

Area of Science:

  • Genomics
  • Bioinformatics

Background:

  • Haplotype phasing is crucial for genotype data analysis.
  • High-throughput sequencing presents new opportunities and challenges for haplotype phasing, especially with low sample numbers and coverage.

Purpose of the Study:

  • To develop a novel algorithm for haplotype phasing that leverages unique properties of high-throughput sequencing data.
  • To address challenges of low sample size and low sequencing coverage in haplotype inference.

Main Methods:

  • Developed the Perfect Phylogeny Haplotypes from Sequencing (PPHS) algorithm.
  • Utilized a perfect phylogeny model and explicitly modeled sequencing errors.
  • Leveraged high SNP density and single-chromosome origin of sequencing reads.

Main Results:

  • PPHS demonstrates superior performance compared to existing methods.
  • The algorithm is particularly effective in high sequencing error rate and low coverage conditions.
  • Evaluated on both real and simulated genomic datasets.

Conclusions:

  • PPHS offers an effective solution for haplotype phasing with modern sequencing technologies.
  • The algorithm advances the inference of haplotypes in challenging low-resource sequencing scenarios.