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

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...
Phylogenetic Trees03:21

Phylogenetic Trees

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.The length of the branches can depict time or the relative amount of change among organisms. For instance, the branch length might indicate the number of amino acid changes in the sequence that underlies the...
Phylogenetic Trees03:21

Phylogenetic Trees

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.The length of the branches can depict time or the relative amount of change among organisms. For instance, the branch length might indicate the number of amino acid changes in the sequence that underlies the...
Phylogeny01:23

Phylogeny

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...
Multi-species Conserved Sequences02:51

Multi-species Conserved Sequences

Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale  studies have provided new insights into the evolutionary relationship between organisms.
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved DNA...
Applications of Molecular Taxonomy01:20

Applications of Molecular Taxonomy

Molecular taxonomy has revolutionized the understanding and classification of bacteria, providing precise insights into their diversity, evolutionary relationships, and ecological roles. By utilizing molecular techniques such as DNA sequencing and fingerprinting, researchers have made significant strides in various fields related to bacterial studies.Resolving Taxonomic AmbiguitiesMolecular taxonomy has been instrumental in distinguishing closely related bacterial species initially thought to...

You might also read

Related Articles

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

Sort by
Same author

Postoperative Celecoxib Associated with Improved Early Continence and Flow-Rates After Holmium Laser Enucleation of the Prostate.

Urology practice·2026
Same author

A <i>Peniophora lycii</i> Isolate Simultaneously Parasitizes <i>Vitis vinefera</i> Host and Associated Fungi, and Possibly Contributes to Grapevine Trunk Disease Development.

Journal of fungi (Basel, Switzerland)·2026
Same author

Ancestral protein sequence reconstruction using a tree-structured Ornstein-Uhlenbeck variational autoencoder.

... International Conference on Learning Representations·2026
Same author

Rapid, accurate long- and short-read mapping to large pangenome graphs with vg Giraffe.

Research square·2025
Same author

Lung-targeting lipid nanoparticle-mediated sparstolonin B delivery improves acute lung injury.

Biomaterials science·2025
Same author

Reply to Editorial Comment on "Delayed Urinary Retention After Holmium Laser Enucleation of Prostate".

Urology·2025

Related Experiment Video

Updated: Jul 2, 2026

A Practical Guide to Phylogenetics for Nonexperts
12:00

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

StatAlign: an extendable software package for joint Bayesian estimation of alignments and evolutionary trees.

Adám Novák1, István Miklós, Rune Lyngsø

  • 1Department of Statistics, University of Oxford, 1 South Parks Road, OX1 3TG Oxford, UK.

Bioinformatics (Oxford, England)
|August 30, 2008
PubMed
Summary

This study introduces user-friendly software for joint phylogenetic and alignment inference, integrating insertions and deletions. The program enhances Bayesian phylogenetic analysis with a graphical interface and flexible models.

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

The ITS2 Database
16:17

The ITS2 Database

Published on: March 12, 2012

Related Experiment Videos

Last Updated: Jul 2, 2026

A Practical Guide to Phylogenetics for Nonexperts
12:00

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
08:57

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

The ITS2 Database
16:17

The ITS2 Database

Published on: March 12, 2012

Area of Science:

  • Computational Biology
  • Bioinformatics
  • Evolutionary Biology

Background:

  • Bayesian analysis is a popular phylogenetic inference method.
  • Current methods often fix alignments, ignoring informative signals from insertions and deletions.
  • A user-friendly program for joint phylogenetic and alignment inference is lacking.

Purpose of the Study:

  • To develop a software package for joint inference of phylogenies and alignments.
  • To implement a user-friendly graphical interface for phylogenetic analysis.
  • To incorporate insertions and deletions as informative signals in phylogenetic reconstruction.

Main Methods:

  • Developed an extendable Java software package.
  • Employed Markov chain Monte Carlo (MCMC) for joint posterior distribution sampling.
  • Integrated models for insertions/deletions with various substitution models.

Main Results:

  • The software enables joint sampling of phylogenies, alignments, and evolutionary parameters.
  • Includes tools for on-the-fly results summarization and postprocessing.
  • Features a graphical interface for analysis configuration, supervision, and result management.

Conclusions:

  • The developed software provides a user-friendly platform for advanced phylogenetic inference.
  • Facilitates the joint analysis of phylogenies and alignments, including insertions and deletions.
  • Offers flexibility through an extendable plugin architecture for new models and analyses.