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

You might also read

Related Articles

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

Sort by
Same author

Palladium-catalyzed olefination and arylation of 2-substituted 1,2,3-triazole N-oxides.

Organic letters·2013
Same author

One-stop hybrid coronary revascularization versus coronary artery bypass grafting and percutaneous coronary intervention for the treatment of multivessel coronary artery disease: 3-year follow-up results from a single institution.

Journal of the American College of Cardiology·2013
Same author

Relative contributions of the thalamus and the paraventricular nucleus of the hypothalamus to the cardiac sympathetic afferent reflex.

American journal of physiology. Regulatory, integrative and comparative physiology·2013
Same author

Initial light soaking treatment enables hole transport material to outperform spiro-OMeTAD in solid-state dye-sensitized solar cells.

Journal of the American Chemical Society·2013
Same author

The rice GERMINATION DEFECTIVE 1, encoding a B3 domain transcriptional repressor, regulates seed germination and seedling development by integrating GA and carbohydrate metabolism.

The Plant journal : for cell and molecular biology·2013
Same author

Salvage intensity modulated radiotherapy using endorectal balloon after radical prostatectomy: clinical outcomes.

International journal of urology : official journal of the Japanese Urological Association·2013
Same journal

The life history of recessive deleterious alleles as seen through the eyes of a honey bee (Apis mellifera).

Molecular biology and evolution·2026
Same journal

Severe bottleneck of ancient Homo populations: Insights from computational modeling and relevant fossil evidence.

Molecular biology and evolution·2026
Same journal

Population Epigenetics: Deciphering DNA Methylation Diversity and its Implications for Health, Disease, and Evolution.

Molecular biology and evolution·2026
Same journal

Genomic signature of repeated transitions to diurnality in spiders.

Molecular biology and evolution·2026
Same journal

Phylogenomic blind spots: The limits of UCE and BUSCO loci in the presence of gene flow.

Molecular biology and evolution·2026
Same journal

seqLens: Optimizing Language Models for Genomic Predictions.

Molecular biology and evolution·2026
See all related articles

Related Experiment Video

Updated: May 7, 2026

gP2S, an Information Management System for CryoEM Experiments
13:01

gP2S, an Information Management System for CryoEM Experiments

Published on: June 10, 2021

5.3K

PAMLX: a graphical user interface for PAML.

Bo Xu1, Ziheng Yang

  • 1Center for Computational Genomics, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.

Molecular Biology and Evolution
|October 10, 2013
PubMed
Summary
This summary is machine-generated.

PAMLX is a new graphical user interface for the Phylogenetic Analysis by Maximum Likelihood (PAML) software. This tool simplifies creating, editing, and running phylogenetic analyses, making complex evolutionary studies more accessible.

Keywords:
molecular evolutionphylogeneticssoftware

More Related Videos

Photoactivated Localization Microscopy with Bimolecular Fluorescence Complementation BiFC-PALM
12:42

Photoactivated Localization Microscopy with Bimolecular Fluorescence Complementation BiFC-PALM

Published on: December 22, 2015

9.4K
Applications for Open Source Microplate-Compatible Illumination Panels
08:48

Applications for Open Source Microplate-Compatible Illumination Panels

Published on: October 3, 2019

7.0K

Related Experiment Videos

Last Updated: May 7, 2026

gP2S, an Information Management System for CryoEM Experiments
13:01

gP2S, an Information Management System for CryoEM Experiments

Published on: June 10, 2021

5.3K
Photoactivated Localization Microscopy with Bimolecular Fluorescence Complementation BiFC-PALM
12:42

Photoactivated Localization Microscopy with Bimolecular Fluorescence Complementation BiFC-PALM

Published on: December 22, 2015

9.4K
Applications for Open Source Microplate-Compatible Illumination Panels
08:48

Applications for Open Source Microplate-Compatible Illumination Panels

Published on: October 3, 2019

7.0K

Area of Science:

  • Computational Biology
  • Evolutionary Biology
  • Bioinformatics

Background:

  • The Phylogenetic Analysis by Maximum Likelihood (PAML) program package is a widely used tool for phylogenetic analysis.
  • Existing PAML usage requires manual creation and editing of control files, which can be complex and error-prone.
  • A user-friendly interface can enhance the accessibility and efficiency of PAML for researchers.

Purpose of the Study:

  • To introduce pamlX, a novel graphical user interface (GUI) for the PAML program package.
  • To provide a more intuitive and efficient workflow for phylogenetic analyses using PAML.
  • To facilitate the creation, editing, and execution of PAML control files.

Main Methods:

  • pamlX is developed in C++ utilizing the Qt library for its graphical interface.
  • The software interacts with PAML programs by generating and managing input files.
  • Functionality includes creating, editing, and printing PAML control files, and launching PAML analyses.

Main Results:

  • pamlX offers a graphical front-end for the PAML software package.
  • The interface simplifies the process of setting up and running phylogenetic analyses.
  • pamlX is freely available for download, promoting wider adoption and use.

Conclusions:

  • pamlX enhances the usability of the PAML program package for phylogenetic analysis.
  • The graphical interface streamlines complex tasks, potentially increasing research productivity.
  • Free accessibility of pamlX encourages broader application in evolutionary biology research.