CoStat 6.45
:: DESCRIPTION
CoStat is an easy-to-use program for data manipulation and statistical analysis.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
- Linux / Mac OsX / Windows
- Java
:: DOWNLOAD
:: MORE INFORMATION
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
:: SCREENSHOTS
:: REQUIREMENTS
- Linux / Mac OsX / Windows
- Java
:: DOWNLOAD
:: MORE INFORMATION
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
:: 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
- Linux
- Perl
- NCBI toolkit
- PSI-BLAST
:: DOWNLOAD
:: 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
:: 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
:: 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
:: SCREENSHOTS
N/A
:: REQUIREMENTS
- Linux
:: DOWNLOAD
:: 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
:: 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.
Pro-origami – Protein Structure Cartoons
Pro-origami
:: DESCRIPTION
Pro-origami is a system for automatically generating protein structure cartoons. The cartoons are intended to make protein structure easy to interpret by laying out the secondary and super-secondary structure in two dimensions in a manner that makes the structure clear.
::DEVELOPER
IALab: Immersive Analytics Lab
:: SCREENSHOTS
N/A
:: REQUIREMENTS
- Linux/ MacOsX / Windows
- Python
- BioPython
- Dunnart
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2011 Dec 1;27(23):3315-6. doi: 10.1093/bioinformatics/btr575.
Automatic generation of protein structure cartoons with Pro-origami.
Stivala A1, Wybrow M, Wirth A, Whisstock JC, Stuckey PJ.
QUANTO 1.2.4 – Computes Sample Size or Power for Association Studies
QUANTO 1.2.4
:: DESCRIPTION
Quanto is a program that computes sample size or power for association studies of genes, environmental factors, gene-environment interaction, or gene-gene interaction. Available study designs for a disease (binary) outcome include the unmatched case-control, matched case-control, case-sibling, case-parent, and case-only designs. Study designs for a quantitative tra it include independent individuals and case parent designs.
::DEVELOPER
The Division of Biostatistics @ usc.edu
:: SCREENSHOTS
:: REQUIREMENTS
- Windows
:: DOWNLOAD
:: MORE INFORMATION
Citation
Gauderman (2002),
“Sample size requirements for matched case-control studies of gene-environment interaction“,
Statistics in Medicine, 21:35-50.