img2net – Automated Network-based Analysis of Imaged Phenotypes

img2net

:: DESCRIPTION

Img2net is a software to automatedly analyze such structures by reconstructing the underlying network, computing relevant network properties, and statistically comparing networks of different types or under different conditions.

::DEVELOPER

Systems biology and Mathematical Modelling

:: SCREENSHOTS

img2net

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Python

:: DOWNLOAD

 Img2net

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Jul 26. pii: btu503.
img2net: automated network-based analysis of imaged phenotypes.
Breuer D, Nikoloski Z.

PICA – Genotype-phenotype data Mining software

PICA

:: DESCRIPTION

PICA (Phenotype Investigation with Classification Algorithms) is a Python framework for testing genotype-phenotype association algorithms.

::DEVELOPER

CUBE – Bioinformatics and Computational Systems Biology, University of Vienna

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 PICA

:: MORE INFORMATION

Citation:

Bioinformatics. 2010 Aug 1;26(15):1834-40. Epub 2010 Jun 6.
Efficient learning of microbial genotype-phenotype association rules.
MacDonald NJ, Beiko RG.

SigniSite 2.1 – Residue level Genotype Phenotype Correlation in Protein Multiple Sequence Alignments

SigniSite 2.1

:: DESCRIPTION

SigniSite performs residue level genotype phenotype correlation in protein multiple sequence alignments by identifying amino acid residues significantly associated with the phenotype of the data set.

::DEVELOPER

DTU Health Tech

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W286-91. doi: 10.1093/nar/gkt497. Epub 2013 Jun 12.
SigniSite: Identification of residue-level genotype-phenotype correlations in protein multiple sequence alignments.
Jessen LE1, Hoof I, Lund O, Nielsen M.

gespeR 0.99.5 – Gene Specific Phenotype Estimator

gespeR 0.99.5

:: DESCRIPTION

gespeR estimates gene-specific phenotypes from off-target confounded RNAi screens. Observed phenotype for a specfic siRNA is modeled as a linear combination of gene-specific phenotypes from the on- and all off-target genes.

::DEVELOPER

the Computational Biology Group (CBG)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • R package

:: DOWNLOAD

 gespeR

:: MORE INFORMATION

Citation

Fabian Schmich, Ewa Szczurek, Saskia Kreibich, Sabrina Dilling, Daniel Andritschke, Alain Casanova, Shyan Huey Low, Simone Eicher, Simone Muntwiler, Mario Emmenlauer, Pauli Ramo, Raquel Conde-Alvarez, Christian von Mering, Wolf-Dietrich Hardt, Christoph Dehio and Niko Beerenwinkel.
gespeR: a statistical model for deconvoluting off-target-confounded RNA interference screens
Genome Biology, 2015.

PPFS 2 – Add on to kSNP for predicting Phenotypes from SNPs in Microbial Genome

PPFS 2

:: DESCRIPTION

The PPFS (Predict Phenotypes From SNPs) package is an add-on to kSNP , a program that can identify SNPs in a data set of hundreds of microbial genomes.

::DEVELOPER

Barry G. Hall

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX

:: DOWNLOAD

PPFS

:: MORE INFORMATION

Citation

PLoS One. 2014 Feb 28;9(2):e90490. doi: 10.1371/journal.pone.0090490. eCollection 2014.
SNP-associations and phenotype predictions from hundreds of microbial genomes without genome alignments.
Hall BG1.

CIPHER – Correlating Protein Interaction Network and Phenotype Network to predict Disease Genes

CIPHER

:: DESCRIPTION

CIPHER, which stands for Correlating interactome and phenome networks to predict disease genes, is a computational framework we proposed to prioritize human disease genes. It was one of the first studies to explore interactome-phenome wide gene-disease relationships, and generated the first comprehensive genetic landscape of human disease,connecting 5080 human disease phenotypes with 14433 human genes.

::DEVELOPER

Wu Lab @ Columbia

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • MatLab

:: DOWNLOAD

NO

 :: MORE INFORMATION

Citation:

Mol Syst Biol. 2008;4:189. doi: 10.1038/msb.2008.27. Epub 2008 May 6.
Network-based global inference of human disease genes.
Wu X1, Jiang R, Zhang MQ, Li S.

PlasmidTron 0.4.1 – Assembling the cause of Phenotypes and Genotypes from NGS data

PlasmidTron 0.4.1

:: DESCRIPTION

PlasmidTron utilizes the phenotypic data normally available in bacterial population studies, such as antibiograms, virulence factors, or geographical information, to identify traits that are likely to be present on DNA that can randomly reassort across defined bacterial populations. It is also possible to use this methodology to associate unknown genes/sequences (e.g. plasmid backbones) with a specific molecular signature or marker (e.g. resistance gene presence or absence) using PlasmidTron. PlasmidTron uses a k-mer-based approach to identify reads associated with a phylogenetically unlinked phenotype.

::DEVELOPER

Pathogen Informatics, Wellcome Trust Sanger Institute

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

PlasmidTron

:: MORE INFORMATION

Citation

PlasmidTron: assembling the cause of phenotypes and genotypes from NGS data,
Andrew J Page, Alexander Wailan, Yan Shao, Kim Judge, Gordon Dougan, Elizabeth J. Klemm, Nicholas R. Thomson, Jacqueline A. Keane, 2018,
Microbial Genomics 4(3); doi: 10.1099/mgen.0.000164

GIPS 1.7 – Gene Identification via Phenotype Sequencing

GIPS 1.7

:: DESCRIPTION

GIPS software considers a range of experimental and analysis choices in sequencing-based forward genetics studies within an integrated probabilistic framework, which enables direct gene cloning from the sequencing of several unrelated mutants of the same phenotype without the need to create segregation populations.

::DEVELOPER

GIPS team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  •  Linux / WIndows/ MacOsX
  • Java

:: DOWNLOAD

 GIPS

:: MORE INFORMATION

Citation

GIPS: A Software Guide to Sequencing-based Direct Gene Cloning in Forward Genetics Studies.
Hu H, Wang W, Zhu Z, Zhu J, Tan D, Zhou Z, Mao C, Chen X.
Plant Physiol. 2016 Feb 3. pii: pp.01327.2015.

SeqSIMLA 2.9.1 – Sequence and Phenotype Simulation tool

SeqSIMLA 2.9.1

:: DESCRIPTION

SeqSIMLA can simulate sequence data in families with multiple affected and unaffected siblings or unrelated case-control under different disease models.

::DEVELOPER

Statistical Genetics and Programming Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows
  • C++ Compiler

:: DOWNLOAD

 SeqSIMLA

:: MORE INFORMATION

Citation

SeqSIMLA2: simulating correlated quantitative traits accounting for shared environmental effects in user-specified pedigree structure.
Chung RH, Tsai WY, Hsieh CH, Hung KY, Hsiung CA, Hauser ER.
Genet Epidemiol. 2015 Jan;39(1):20-4. doi: 10.1002/gepi.21850.

eCOMPAGT 20140910 – efficient COmbination and Management of Phenotypes and GenoTypes

eCOMPAGT 20140910

:: DESCRIPTION

eCOMPAGT is an application for the efficient COmbination and Management of Phenotypes. eCOMPAGT can store, administer and connect phenotype data with all kinds of genotype data.

::DEVELOPER

GenEpi – Division of Genetic Epidemiology Innsbruck

:: SCREENSHOTS

eCOMPAGT

:: REQUIREMENTS

  • Windows/Linux

:: DOWNLOAD

 eCOMPAGT

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2010 Mar 9;11:122. doi: 10.1186/1471-2105-11-122.
eCOMPAGT integrates mtDNA: import, validation and export of mitochondrial DNA profiles for population genetics, tumour dynamics and genotype-phenotype association studies.
Weissensteiner H1, Schönherr S, Specht G, Kronenberg F, Brandstätter A.