SimPed – Generate Haplotype and Genotype data for Pedigree Structures

SimPed

:: DESCRIPTION

SimPed is a program that quickly generates haplotypes and/or genotype data for a large number of marker loci (>20,000) for pedigrees of virtually any size and complexity. Haplotypes and/or genotypes are generated using user specified genetic map distances and haplotypes and/or allele frequencies.

::DEVELOPER

Human Genome Sequencing Center

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows  / Linux / MacOsX

:: DOWNLOAD

 SimPed

:: MORE INFORMATION

Citation

Leal, Yan, Muller-Myhsok (2005),
SimPed: a simulation program to generate haplotype and genotype data for pedigree structures“,
Human Heredity, 60(2):119-122.

ESPript 3.0.5 / ENDscript 2.0.5 – Generate Pretty PostScript Output from Aligned Sequences

ESPript 3.0.5 / ENDscript 2.0.5

:: DESCRIPTION

ESPript (Easy Sequencing in Postscript) is a utility to generate a pretty PostScript output from aligned sequences.

ENDscript is an interface grouping eight types of Programs:  BLAST;  MULTALIN/  CLUSTALW;  DSSP;  CNS;  ESPript;  BOBSCRIPTMOLSCRIPT;  DINO;  PHYLODENDRON;  PROFIT.

ESPript Online Version

::DEVELOPER

Patrice Gouet and Frédéric Metoz.  Emmanuel Courcelle. Xavier Robert

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 ESPript/ ENDscript

:: MORE INFORMATION

Citation

Gouet, P., Courcelle, E., Stuart, D.I. and Metoz, F. (1999).
ESPript: analysis of multiple sequence alignments in PostScript
Bioinformatics. 15 305-8

Nucleic Acids Res. 2003 Jul 1;31(13):3320-3.
ESPript/ENDscript: Extracting and rendering sequence and 3D information from atomic structures of proteins.
Gouet P, Robert X, Courcelle E.

SBMLsqueezer 2.1 – Generate Kinetic Equations for Biochemical Networks

SBMLsqueezer 2.1

:: DESCRIPTION

SBMLsqueezer generates kinetic equations for biochemical networks according to context of each reaction. When used as a plugin for CellDesigner it uses the information from the SBGN representation of all network components. In the stand-alone mode, SBMLsqueezer evaluates the Systems Biology Ontology (SBO) annotations to extract this information.

The rate laws that can be produced by SBMLsqueezer include several types of generalized mass action; detailed and generalized enzyme kinetics, various types of Hill equations, S- and H-systems, and additive models for gene regulation. User defined settings specify which equation to apply for any type of reaction and how to ensure unit consistency of the model. Equations can be created using contextual menus. All newly created parameters are equipped with the derived unit and annotated with SBO terms if available and meaningful textual names. MathML is inserted directly into the SBML file. LaTeX or text export of ordinary differential equations is provided.

::DEVELOPER

Dr. Andreas Dräger

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

SBMLsqueezer

:: MORE INFORMATION

Citation

SBMLsqueezer: a CellDesigner plug-in to generate kinetic rate equations for biochemical networks.
Dräger A, Hassis N, Supper J, Schröder A, Zell A.
BMC Syst Biol. 2008 Apr 30;2:39. doi: 10.1186/1752-0509-2-39.

PRINSEQ 0.20.4 – Preprocess and Generate Statistics about Sequence data

PRINSEQ 0.20.4

:: DESCRIPTION

PRINSEQ (PReprocessing and INformation of SEQuence data.) is a tool that generates summary statistics of sequence and quality data and that is used to filter, reformat and trim next-generation sequence data. It is particular designed for 454/Roche data, but can also be used for other types of sequence data. PRINSEQ is available through a user-friendly web interface or as standalone version. The standalone version is primarily designed for data preprocessing and does not generate summary statistics in graphical form.

PRINSEQ Online Version

::DEVELOPER

the Edwards Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Mac OsX / Linux /
  • Perl

:: DOWNLOAD

 PRINSEQ

:: MORE INFORMATION

Citation:

Schmieder R and Edwards R
Quality control and preprocessing of metagenomic datasets.
Bioinformatics 2011, 27:863-864.

SHiAT 1.1 – Generates Plots of Variation along Sequence Alignment

SHiAT 1.1

:: DESCRIPTION

SHiAT (Shannon Heterogeneity in Alignments Tool) provides an intuitive graphical interface for the simultaneous calculation of three measures of sitewise variation in DNA or RNA alignments. The Shannon Information index, Hamming distance and (1-consensus frequency) are all calculated and displayed in a series of graphical plots. Multiple alignments may be imported and compared, and a data view panel allows easy copy-and-pasting into external applications.

::DEVELOPER

Joe Parker

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • Java

:: DOWNLOAD

SHiAT

:: MORE INFORMATION

Molgenis 15.04 – Generate Databases for Life Science Experiments

Molgenis 15.04

:: DESCRIPTION

MOLGENIS ( MOLecular GENetics Information Systems) is an collaborative open source project on a mission to generate great software infrastructure for life science research. Each app in the MOLGENIS family comes with rich data management interface and plug-in integration of analysis tools in R, Java and web services. The MOLGENIS platform allows you to automatically generate rich database software to your specifications, including web user interfaces to manage and query your data, various database back ends to store your data, and programmatic interfaces to the R language and web services. You tell MOLGENIS what to generate using an data model and user interface model described in XML; at the push of a button MOLGENIS translates this model into SQL, Java and R program files. Also documentation is generated. While the standard generated MOLGENIS is sufficient for most data management needs, MOLGENIS also allows you to plug in handwritten software components that build on the auto-generated software platform.

::DEVELOPER

the Genomics Coordination Centre

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 Molgenis 

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2010 Dec 21;11 Suppl 12:S12.
The MOLGENIS toolkit: rapid prototyping of biosoftware at the push of a button.
Swertz MA, Dijkstra M, Adamusiak T, van der Velde JK, Kanterakis A, Roos ET, Lops J, Thorisson GA, Arends D, Byelas G, Muilu J, Brookes AJ, de Brock EO, Jansen RC, Parkinson H.

savvy 0.1 – Generate High Resolution Print Quality Plasmid Map

savvy 0.1

:: DESCRIPTION

savvy is a CGI web app to generate high resolution print quality plasmid map using SVG.

::DEVELOPER

Malay K Basu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 savvy

:: MORE INFORMATION

OGdraw 1.1.1 – Generate high-quality Graphical Maps of circular DNA Sequences

OGdraw 1.1.1

:: DESCRIPTION

OGDraw (OrganelleGenomeDraw) is a tool that enables the user to quickly generate high-quality graphical maps of circular DNA sequences. Though especially designed and optimized for the display of small organelle genomes like the chloroplast or mitochondrial genome, it is applicable to all circular DNA sequences. The input data can be provided as GenBank files or GenBank accession numbers.

::DEVELOPER

Max Planck Institute for Molecular Plant Physiology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX/Windows
  • Perl

:: DOWNLOAD

 OGdraw

:: MORE INFORMATION

Citation

Curr Genet. 2007 Nov;52(5-6):267-74. Epub 2007 Oct 24.
OrganellarGenomeDRAW (OGDRAW): a tool for the easy generation of high-quality custom graphical maps of plastid and mitochondrial genomes.
Lohse M, Drechsel O, Bock R.

McQSAR 1.2.4.83 – Generate Quantitative Structure-activity Relationships

McQSAR 1.2.4.83

:: DESCRIPTION

McQSAR generates quantitative structure-activity relationships (QSARs) using the genetic function approximation paradigm.

::DEVELOPER

Structural Bioinformatics Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX

:: DOWNLOAD

  McQSAR

:: MORE INFORMATION

Citation:

Mikko J. Vainio and Mark S. Johnson (2005)
McQSAR: A Multiconformational Quantitative Structure-Activity Relationship Engine Driven by Genetic Algorithms.
J. Chem. Inf. Model. 45, 1953-1961.

RMAExpress 1.1.0 – Generate RMA Expression Measures for Affy data

RMAExpress 1.1.0

:: DESCRIPTION

RMAExpress is a standalone GUI program for Windows (and Linux) to compute gene expression summary values for Affymetrix Genechip® data using the Robust Multichip Average expression summary and to carry out quality assessment using probe-level metrics.

::DEVELOPER

Ben Bolstad

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/ MacOsX / Windows

:: DOWNLOAD

 RMAExpress

:: MORE INFORMATION