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.

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

Pro-origami

:: 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

QUANTO

:: MORE INFORMATION

Citation

Gauderman (2002),
“Sample size requirements for matched case-control studies of gene-environment interaction“,
Statistics in Medicine, 21:35-50.

METASOFT 2.0.1 – Meta-analysis Tool

METASOFT 2.0.1

:: DESCRIPTION

METASOFT is a meta-analysis software tool for genome-wide association studies that provides the following methods

Fixed Effects model (FE): Fixed effects model based on inverse-variance-weighted effect size.
Random Effects model (RE): Conventional random effects model based on inverse-variance-weighted effect size. Heterogeneity is estimated using DerSimonian-Laird method.
Han and Eskin’s Random Effects model (RE2): Random effects model that increases power under heterogeneity.
Binary Effects model (BE): Random effects model assuming that the effects either exist or not in the studies.

::DEVELOPER

ZarLab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Mac OsX / Windows
Java

:: DOWNLOAD

METASOFT

:: MORE INFORMATION

Citation

Buhm Han and Eleazar Eskin,
“Random-Effects Model Aimed at Discovering Associations in Meta-Analysis of Genome-wide Association Studies”,
The American Journal of Human Genetics (2011) 88, 586-598.

Panache v1.0.0 – PANgenome Analyzer with CHromosomal Exploration

Panache v1.0.0

:: DESCRIPTION

Panache is a web-based interface designed for the visualization of linearized pangenomes. It can be used to show presence/absence information of pangenomic blocks of sequence or genes in a browser-like display.

::DEVELOPER

Panache team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

Durant É, Sabot F, Conte M, Rouard M.
Panache: a Web Browser-Based Viewer for Linearized Pangenomes.
Bioinformatics. 2021 Oct 2:btab688. doi: 10.1093/bioinformatics/btab688. Epub ahead of print. PMID: 34601567.