raxmlGUI 2.0.0b2 – A new Graphical Interface for RAxML

raxmlGUI 2.0.0b2

:: DESCRIPTION

raxmlGUI is a graphical user interface to RAxML, one of the most popular and widely used software for phylogenetic inference using maximum likelihood.

::DEVELOPER

Antonelli Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • RAxML

:: DOWNLOAD

raxmlGUI

:: MORE INFORMATION

Citation

Edler, D., Klein, J., Antonelli, A., and Silvestro, D. 2019.
raxmlGUI 2.0 beta: a graphical interface and toolkit for phylogenetic analyses using RAxML.
bioRxiv, doi: https://doi.org/10.1101/800912

MetaReg – Graphical Interface for Modeling and Evaluation of Biological Systems

MetaReg.

:: DESCRIPTION

MetaReg is a Java application aimed to provide the biologist with an intuitive graphical interface for both definition and analysis of system models. The application makes it possible to navigate the model network and compare its predicted and observed behavior.

::DEVELOPER

Prof. Ron Shamir’s Computational Genomics Group at Tel Aviv University.

:: SCREENSHOTS

::REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java

:: DOWNLOAD

 MetaReg

:: MORE INFORMATION

Citation

I. Gat-Viks and R. Shamir.
MetaReg application: a graphical interface for modeling and evaluation of biological systems.
Genome Biology (2008) Vol. 9 No. R1

KymoRod 0.10.0 – Matlab Graphical Interface for the Study of Hypocotyl Growth

KymoRod 0.10.0

:: DESCRIPTION

KymoRod is a method for automated kinematic analysis of rod-shaped plant organs.

::DEVELOPER

IJPB Modeling and digital imaging lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • MatLab

:: DOWNLOAD

 KymoRod

:: MORE INFORMATION

Citation

KymoRod: A method for automated kinematic analysis of rod-shaped plant organs.
Bastien R, Legland D, Martin M, Fregosi L, Peaucelle A, Douady S, Moulia B, Höfte H.
Plant J. 2016 Jun 29. doi: 10.1111/tpj.13255.

VisualModuleOrganizer 1.0 / ModuleOrganizer 2 – Graphical Interface for/ Detection and Comparative Analysis of Repeat DNA Modules

VisualModuleOrganizer 1.0/ ModuleOrganizer 2

:: DESCRIPTION

ModuleOrganizer detects repeated modules in sequences and allows comparative and evolutionary analysis of these elements.Visual ModuleOrganizer is a JAVA graphical interface that displays graphical results from the new embedded version of ModuleOrganizer and allows easy handling of the results.

::DEVELOPER

Biophotonics Lab

:: SCREENSHOTS

VisualModuleOrganizer

:: REQUIREMENTS

  • Linux/ Windows / MacOsX
  • Java Runtime Environment (JRE)

:: DOWNLOAD

 Visual ModuleOrganizer , ModuleOrganizer

:: MORE INFORMATION

Citation

Mob DNA. 2014 Mar 28;5:9. doi: 10.1186/1759-8753-5-9. eCollection 2014.
Visual ModuleOrganizer: a graphical interface for the detection and comparative analysis of repeat DNA modules.
Tempel S, Talla E.

BMC Bioinformatics. 2010 Sep 22;11:474. doi: 10.1186/1471-2105-11-474.
ModuleOrganizer: detecting modules in families of transposable elements.
Tempel S1, Rousseau C, Tahi F, Nicolas J.

VisualTE 1.02 – Graphical Interface for Transposable Element Analysis at Genomic Scale

VisualTE 1.02

:: DESCRIPTION

VisualTE is a JAVA stand-alone graphical interface that allows users to visualize and analyze all occurrences of transposable element families in annotated genomes.

::DEVELOPER

Biophotonics Lab

:: SCREENSHOTS

VisualTE

:: REQUIREMENTS

  • Linux/ Windows / MacOsX
  • Java Runtime Environment (JRE)

:: DOWNLOAD

 VisualTE

:: MORE INFORMATION

Citation

VisualTE: a graphical interface for transposable element analysis at the genomic scale.
Tempel S, Talla E.
BMC Genomics. 2015 Feb 27;16:139. doi: 10.1186/s12864-015-1351-5.

gPLINK 2.050 – Graphical Interface for PLINK

gPLINK 2.050

:: DESCRIPTION

gPLINK is a Java program that provides a simple form interface to the more commonly-used PLINK commands (i.e. instead of using the command line options). gPLINK provides menus and dialogs to create valid PLINK commands, executes them, keeps a record of all commands run in a project, keeps track of input and output files, allows annotation of result files and facilitates integration with Haploview.

::DEVELOPER

Purcell Lab

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 gPLINK

:: MORE INFORMATION

Citation

Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MAR, Bender D, Maller J, Sklar P, de Bakker PIW, Daly MJ & Sham PC (2007)
PLINK: a toolset for whole-genome association and population-based linkage analysis. 
American Journal of Human Genetics, 81.