GeneNetWeaver 3.1.3 Beta – in silico benchmark Generation and performance profiling of Network Inference Methods

GeneNetWeaver 3.1.3 Beta

:: DESCRIPTION

GeneNetWeaver (GNW) is an open-source tool for in silico benchmark generation and performance profiling of network inference methods.

::DEVELOPER

GeneNetWeaver team

:: SCREENSHOTS

GeneNetWeaver

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Java

:: DOWNLOAD

 GeneNetWeaver

:: MORE INFORMATION

Citation:

Schaffter, T. et al. (2011).
GeneNetWeaver: In silico benchmark generation and performance profiling of network inference methods.
Bioinformatics, 27(16):2263-70

MEDELLER – Homology-Based Coordinate Generation for Membrane Proteins

MEDELLER

:: DESCRIPTION

MEDELLER, a MP(Membrane proteins)-specific homology-based coordinate generation method,  which is optimized to build highly reliable core models.

::DEVELOPER

the Oxford Protein Informatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Bioinformatics. 2010 Nov 15;26(22):2833-40. doi: 10.1093/bioinformatics/btq554. Epub 2010 Oct 5.
MEDELLER: homology-based coordinate generation for membrane proteins.
Kelm S, Shi J, Deane CM.

DecoyDatabaseBuilder 1.5.47 – Generation of Decoy Sequences for Amino Acid Databases

DecoyDatabaseBuilder 1.5.47

:: DESCRIPTION

DecoyDatabaseBuilder is a module of the PeakQuant suite, it enables the generation of decoy sequences for amino acid databases.

::DEVELOPER

Medizinisches Proteom-Center, Medical Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • JRE

:: DOWNLOAD

 DecoyDatabaseBuilder

:: MORE INFORMATION

Citation

Proteomics. 2008 Mar;8(6):1129-37. doi: 10.1002/pmic.200701073.
An easy-to-use Decoy Database Builder software tool, implementing different decoy strategies for false discovery rate calculation in automated MS/MS protein identifications.
Reidegeld KA1, Eisenacher M, Kohl M, Chamrad D, Körting G, Blüggel M, Meyer HE, Stephan C.

PhyloPro – Generation and Visualization of Phylogenetic Profiles across Eukarya

PhyloPro

:: DESCRIPTION

PhyloPro allows the user to rapidly identify core conserved elements of biological processes together with those that may represent lineage-specific innovations.

::DEVELOPER

Parkinson lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Mar 15;27(6):877-8. doi: 10.1093/bioinformatics/btr023. Epub 2011 Jan 19.
PhyloPro: a web-based tool for the generation and visualization of phylogenetic profiles across Eukarya.
Xiong X, Song H, On T, Lochovsky L, Provart NJ, Parkinson J.

WhatsHap – Haplotype Assembly for Future-Generation Sequencing Reads

WhatsHap

:: DESCRIPTION

WhatsHap is a software for phasing genomic variants using DNA sequencing reads, also called haplotype assembly. It is especially suitable for long reads, but works also well with short reads.

::DEVELOPER

The Algorithms for Computational Genomics group 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python
  • C++

:: DOWNLOAD

 WhatsHap

:: MORE INFORMATION

Citation

WhatsHap: Weighted Haplotype Assembly for Future-Generation Sequencing Reads.
Patterson M, Marschall T, Pisanti N, van Iersel L, Stougie L, Klau GW, Schönhuth A.
J Comput Biol. 2015 Jun;22(6):498-509. doi: 10.1089/cmb.2014.0157

MOLGEN 5.0 – Molecular Structure Generation

MOLGEN 5.0

:: DESCRIPTION

The program system MOLGEN is devoted to generating all structures (connectivity isomers, constitutions) that correspond to a given molecular formula, with optional further restrictions, e.g. presence or absence of particular substructures. The project arose in 1985 from the idea to provide an efficient and portable tool for molecular structure elucidation in chemical industry, research, and education.

::DEVELOPER

MOLGEN Team

:: SCREENSHOTS

MOLGEN

:: REQUIREMENTS

  • Windows/Linux

:: DOWNLOAD

 MOLGEN

:: MORE INFORMATION

R. Gugisch, A. Kerber, A. Kohnert, R. Laue, M. Meringer, C. Rücker, A. Wassermann :
MOLGEN 5.0, a Molecular Structure Generator.
Submitted to Bentham Science Publishers Ltd. 2012

AgeStructure 1.0 – Estimate Effective Size & Generation Interval of Population with overlapping Generations

AgeStructure 1.0

:: DESCRIPTION

AgeStructure is a computer program for estimating the generation interval, effective size, variances and covariances of lifetime number of offspring of an age structured population with overlapping generations.

:: DEVELOPER

Dr Jinliang Wang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • Fortran 90/95 compiler

:: DOWNLOAD

 AgeStructure

:: MORE INFORMATION

Citation

Wang, J., Brekke, P. , Huchard, E., Knapp, L. A. , Cowlishaw, G. 2010.
Estimation of parameters of inbreeding and genetic drift in populations with overlapping generations.
Evolution, 64, 1704–1718.

Pajek Writer – Generation of Structural Representation of Biochemical Processes in Format Pajek

Pajek Writer

:: DESCRIPTION

Pajek Writer – software for generation of structural representation of biochemical processes in format Pajek on a set of the proceeding reactions presented in the form of the list of biochemical reactions.

::DEVELOPER

Group of Molecular Genetic Systems Modeling

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux
  • Java

:: DOWNLOAD

 Pajek Writer

:: MORE INFORMATION

jagn 1.02 – Java-Based Model for Artificial Gene Networks Generation

jagn 1.02

:: DESCRIPTION

jagn is a software for an Artificial Gene Networks (AGNs) model generation through theoretical models of complex networks, which is used to simulate temporal expression data, which can be used by computational methods to recover the network topology, and then, analyse the results based on complex networks measurements/topology.

::DEVELOPER

Fabrício Martins Lopes

:: SCREENSHOTS

jagn

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java

:: DOWNLOAD

  jagn

:: MORE INFORMATION

Citation:

Lopes, Fabrício M.; Cesar-Jr, Roberto M.; Costa, Luciano da F.
Gene expression complex networks: synthesis, identification and analysis.
Journal of Computational Biology, v. 18, p. 1353-1367, 2011.

TagGD – DNA Tag Generation and Demultiplexing

TagGD

:: DESCRIPTION

TagGD (DNA-based Tag Generator and Demultiplexor), a fully-customisable, fast and accurate software package that can generate thousands of barcodes satisfying user-defined constraints and can guarantee full demultiplexing accuracy.

::DEVELOPER

Pelin Akan (Phone: 0852481452)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX/Windows

:: DOWNLOAD

  TagGD

:: MORE INFORMATION

Citation

PLoS One. 2013;8(3):e57521. doi: 10.1371/journal.pone.0057521. Epub 2013 Mar 4.
TagGD: fast and accurate software for DNA Tag generation and demultiplexing.
Costea PI, Lundeberg J, Akan P.