Gromita 4.6 – GUI for GROMACS

Gromita 4.6

:: DESCRIPTION

Gromita is a Graphical User Interface (GUI) for GROMACS (v.3 and 4). It is writen in perl making extensive use of perl/tk achieving portability in a wide variety of operating systems and architectures. Gromita provides friendly to use buttons in a windows-based environment while maintaining a terminal mode for the experienced user.

::DEVELOPER

Gromita Team

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 Gromita

:: MORE INFORMATION

Citation

Sellis D, Vlachakis D, Vlassi M. (2009)
Gromita: A Fully Integrated Graphical User Interface to Gromacs 4.
Bioinform Biol Insights 2009:3 99-102

Desmond 2023.2 – High-speed Molecular Dynamics Simulation

Desmond 2023.2

:: DESCRIPTION

Desmond is a software package developed at D. E. Shaw Research to perform high-speed molecular dynamics simulations of biological systems on conventional commodity clusters. The code uses novel parallel algorithms and numerical techniques to achieve high performance and accuracy on platforms containing a large number of processors, but may also be executed on a single computer.

::DEVELOPER

D. E. Shaw Research

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Window / Linux / Mac OsX
  • Python

:: DOWNLOAD

Desmond

:: MORE INFORMATION

Citation

Kevin J. Bowers, Edmond Chow, Huafeng Xu, Ron O. Dror, Michael P. Eastwood, Brent A. Gregersen, John L. Klepeis, István Kolossváry, Mark A. Moraes, Federico D. Sacerdoti, John K. Salmon, Yibing Shan, and David E. Shaw,
“Scalable Algorithms for Molecular Dynamics Simulations on Commodity Clusters,”
Proceedings of the ACM/IEEE Conference on Supercomputing (SC06), Tampa, Florida, November 11–17, 2006

CoPlot 6.45 – Software for Great Scientific Graphs, Maps, and Technical Drawings

CoPlot 6.45

:: DESCRIPTION

CoPlot is an incredibly versatile program for making publication-quality 2D and 3D scientific graphs (which plot data and equations), maps, and technical drawings. Every aspect of CoPlot has been designed around one basic goal: to make a program that is so versatile that scientists and engineers can easily get exactly what they want. CoPlot includes CoStat for data handling and statistics.

::DEVELOPER

CoHort Software

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Mac OsX / Windows
  • Java

:: DOWNLOAD

CoPlot

:: MORE INFORMATION

Order

SplitsTree 6.1.10 – Compute Phylogenetic Networks

SplitsTree 6.1.10

:: DESCRIPTION

SplitsTree uses the split decomposition method to analyse and visualize distance data, e.g. data derived from biosequences. SplitsTree4 is the leading application for computing unrooted phylogenetic networks from molecular sequence data. Given an alignment of sequences, a distance matrix or a set of trees, the program will compute a phylogenetic tree or network using methods such as split decomposition, neighbor-net, consensus network, super networks methods or methods for computing hybridization or simple recombination networks.

::DEVELOPER

the Algorithms in Bioinformatics lab.

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / Mac OsX

:: DOWNLOAD

SplitsTree

:: MORE INFORMATION

Citation

D. H. Huson and D. Bryant,
Application of Phylogenetic Networks in Evolutionary Studies
Mol. Biol. Evol., 23(2):254-267, 2006.

PSIPRED 4.02 – Accurate Protein Secondary Structure Prediction

PSIPRED 4.02

:: DESCRIPTION

PSIPRED (Position Specific Iterated Prediction) is a highly accurate method for protein secondary structure prediction.

Bioinformatics Group – University College London

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 PSIPRED

:: MORE INFORMATION

Citation:

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W349-57. doi: 10.1093/nar/gkt381. Epub 2013 Jun 8.
Scalable web services for the PSIPRED Protein Analysis Workbench.
Buchan DW1, Minneci F, Nugent TC, Bryson K, Jones DT.

Bioinformatics. 2000 Apr;16(4):404-5.
The PSIPRED protein structure prediction server.
McGuffin LJ, Bryson K, Jones DT.

Breeder 3.0 – Plant Breeding Game

Breeder 3.0

:: DESCRIPTION

Breeder is an entertaining plant breeding game, that puts you in the position of the breeder that has to make selection with a limited amount of resources. Can you obtain the tallest plants with the right color.

The engine of the game is a realistic (Mendelian) genetic model with linkage and recombination, topped off with some random noise.

::DEVELOPER

The expertise group Plant Breeding

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

Breeder

:: MORE INFORMATION

Flapjack 1.22.04.21 – Graphical Genotype Visualization

Flapjack 1.22.04.21

:: DESCRIPTION

Flapjack is a new software tool for graphical genotyping and haplotype visualization which is required that can routinely handle the large data volumes generated by high throughput SNP and comparable genotyping technologies. Flapjack is a new visualization tool to facilitate analysis of these data types. Its visualizations are rendered in real-time allowing for rapid navigation and comparisons between lines, markers and chromosomes.

::DEVELOPER

Information & Computational Sciences, The James Hutton Institute

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOSX
  • Java

:: DOWNLOAD

 Flapjack

:: MORE INFORMATION

Citation

Iain Milne etc.
Flapjack – Graphical Genotype Visualization
Bioinformatics (2010)doi : 10.1093/bioinformatics/btq580

FoldX 3.0 – Force Field for Energy Calculations and Protein Design

FoldX 3.0

:: DESCRIPTION

FoldX conduct rapid evaluation of the effect of mutations on the stability, folding and dynamics of proteins and nucleic acids.

The FoldX/Yasara ( FoldX plugin for YASARA) is a software package to access and run FoldX commands in YASARA.

::DEVELOPER

Serrano’s laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 FoldX

:: MORE INFORMATION

Citation

The FoldX web server: an online force field.
Schymkowitz J, Borg J, Stricher F, Nys R, Rousseau F, Serrano L.
Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W382-8.

IRF 3.07 – Inverted Repeats Finder

IRF 3.07

:: DESCRIPTION

IRF(Inverted Repeats Finder) investigate inverted repeat structure of the Human Genome

::DEVELOPER

Laboratory for Biocomputing and Informatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX

:: DOWNLOAD

 IRF

:: MORE INFORMATION

Citation:

P. E. Warburton, J. Giordano, F. Cheung, Y. Gelfand and G. Benson.
“Inverted Repeat Structure of the Human Genome: The X-Chromosome Contains a Preponderance of Large, Highly Homologous Inverted Repeats That Contain Testes Genes” ,
Genome Research, 14:1861-1869, 2004.