Coevol 1.5 – Correlated Evolution of Substitution Rates and Phenotypes

Coevol 1.5

:: DESCRIPTION

Coevol is a Bayesian MCMC software for comparative analyses combining molecular data and continuous characters (e.g. ecological variables or life-history traits.)

::DEVELOPER

Nicolas Lartillot (nicolas.lartillot@umontreal.ca)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / Mac OsX

:: DOWNLOAD

 Coevol

:: MORE INFORMATION

Citation

Lartillot N, Poujol R.
A phylogenetic model for investigating correlated evolution of substitution rates and continuous phenotypic characters.
Mol Biol Evol. 2011 Jan;28(1):729-44. Epub 2010 Oct 6.

MamPhEA – Mammalian Phenotype Enrichment Analysis

MamPhEA

:: DESCRIPTION

MamPhEA is a web application dedicated to understanding functional properties of mammalian gene sets based on mouse-mutant phenotypes.

::DEVELOPER

MamPhEA team

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Bioinformatics. 2010 Sep 1;26(17):2212-3. doi: 10.1093/bioinformatics/btq359. Epub 2010 Jul 6.
MamPhEA: a web tool for mammalian phenotype enrichment analysis.
Weng MP1, Liao BY.

PINES – Phenotype-Informed Noncoding Element Scoring

PINES

:: DESCRIPTION

PINES evaluates the functional impact of noncoding variants by integrating diverse epigenetic annotations, utilizing genomic annotations most relevant to phenotypes of interest.

::DEVELOPER

SUNYAEV LAB

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux
  • R

:: DOWNLOAD

PINES

:: MORE INFORMATION

Citation

Bodea CA, Mitchell AA, Bloemendal A, Day-Williams AG, Runz H, Sunyaev SR.
PINES: phenotype-informed tissue weighting improves prediction of pathogenic noncoding variants.
Genome Biol. 2018 Oct 25;19(1):173. doi: 10.1186/s13059-018-1546-6. PMID: 30359302; PMCID: PMC6203199.

SIMLAPLOT 1.0 – Visualize Genotype and Phenotype Relationship

SIMLAPLOT 1.0

:: DESCRIPTION

SIMLAPLOT is a software for visualizing different ways in which continuous covariates may influence the genotype-specific risk for complex human diseases. The purpose of our study was to examine continuous covariates in the Genetic Analysis Workshop 15 simulated data set using our novel graphical display tool, with knowledge of the answers. The generated plots provide information about genetic models for the simulated continuous covariates and may help identify the single-nucleotide polymorphisms associated with the underlying quantitative trait loci.

::DEVELOPER

Duke Molecular Physiology Institute

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 SIMLAPLOT

:: MORE INFORMATION

Citation

Xuejun Qin,et al
Visualizing genotype × phenotype relationships in the GAW15 simulated data
BMC Proc. 2007; 1(Suppl 1): S132.

GENOSIM v4 – Simulate Genotypes, Breeding Values, and Phenotypes

GENOSIM v4

:: DESCRIPTION

GENOSIM is a set of programs to simulate genotypes, breeding values, phenotypes, and DNA sequence read depth and to resolve SNP conflicts between parent and offspring genotypes

::DEVELOPER

Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Fortron

:: DOWNLOAD

  GENOSIM

:: MORE INFORMATION

dbVOR 1.12 – Phenotype and Genotype Database System

dbVOR 1.12

:: DESCRIPTION

dbVOR is a database system for importing pedigree, phenotype and genotype data and exporting selected subsets.

::DEVELOPER

Division of Statistical Genetics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python
  • MySQL
  • MySQLDB

:: DOWNLOAD

 dbVOR

:: MORE INFORMATION

Citation

dbVOR: a database system for importing pedigree, phenotype and genotype data and exporting selected subsets
Baron RV, Conley YP, Gorin MB, Weeks DE.
BMC Bioinformatics. 2015 Mar 18;16(1):91.

CRaVe 0.0.2 – Association Tests between sets of SNPs and a Phenotype

CRaVe 0.0.2

:: DESCRIPTION

CRaVe is a free, open source, software package designed to perform a range of association tests between sets of SNPs and a phenotype.

::DEVELOPER

 DCEG

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • R package

:: DOWNLOAD

 CRaVe

:: MORE INFORMATION

Citation

Eur J Hum Genet. 2013 Jun;21(6):680-6. doi: 10.1038/ejhg.2012.220. Epub 2012 Oct 24.
Statistical tests for detecting associations with groups of genetic variants: generalization, evaluation, and implementation.
Ferguson J, Wheeler W, Fu Y, Prokunina-Olsson L, Zhao H, Sampson J.

CPAG 0.2 – Cross-Phenotype Analysis of GWAS

CPAG 0.2

:: DESCRIPTION

CPAG can estimate disease and trait similarity, identify informative disease clusters, and carry out pathway enrichment analysis. It also provides visualization of these results in the form of hierarchical clustering trees, heatmaps, and networks.

::DEVELOPER

Rawls Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOS

:: DOWNLOAD

 CPAG

:: MORE INFORMATION

Citation:

CPAG: software for leveraging pleiotropy in GWAS to reveal similarity between human traits links plasma fatty acids and intestinal inflammation.
Wang L, Oehlers SH, Espenschied ST, Rawls JF, Tobin DM, Ko DC.
Genome Biol. 2015 Sep 15;16:190. doi: 10.1186/s13059-015-0722-1.

JEPEG 0.2.0 / JEPEGMIX 0.1.0 – Joint Effect on Phenotype of eQTLs/functional SNPs associated with a Gene

JEPEG 0.2.0 /JEPEGMIX 0.1.0

:: DESCRIPTION

JEPEG is a novel software which uses only summary statistics and correlation structures estimated from a reference popluation, to i) impute the summary statistics at unmeasured eQTLs and ii) test for the joint effect of measured and imputed all eQTLs affecting a gene function/expression on a phenotype.

JEPEGMIX is a JEPEG extension for gene-level joint testing of functional variants.

::DEVELOPER

dleelab.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 JEPEG , JEPEGMIX

:: MORE INFORMATION

Citation

JEPEGMIX: gene-level joint analysis of functional SNPs in cosmopolitan cohorts.
Lee D, Williamson VS, Bigdeli TB, Riley BP, Webb BT, Fanous AH, Kendler KS, Vladimirov VI, Bacanu SA.
Bioinformatics. 2015 Oct 1. pii: btv567

JEPEG: a summary statistics based tool for gene-level joint testing of functional variants.
Lee D, Williamson VS, Bigdeli TB, Riley BP, Fanous AH, Vladimirov VI, Bacanu SA.
Bioinformatics. 2014 Dec 12. pii: btu816

Bubble GUM 1.3.19 – Extraction of Phenotype Molecular Signatures and Comprehensive Visualization

Bubble GUM 1.3.19

:: DESCRIPTION

Bubble GUM (GSEA Unlimited Map) is a computational tool that allows to automatically extract phenotype signatures based on transcriptomic data and to perform easily multiple GSEA runs in a row.

::DEVELOPER

Centre d’Immunologie, de Marseille-Luminy

:: SCREENSHOTS

BubbleGUM

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Java

:: DOWNLOAD

 Bubble GUM

:: MORE INFORMATION

Citation

BubbleGUM: automatic extraction of phenotype molecular signatures and comprehensive visualization of multiple Gene Set Enrichment Analyses.
Spinelli L, Carpentier S, Montañana Sanchis F, Dalod M, Vu Manh TP.
BMC Genomics. 2015 Oct 19;16(1):814. doi: 10.1186/s12864-015-2012-4.