:: DESCRIPTION
iBPP is a program of integration of genes and traits for Bayesian Phylogenetics and Phylogeography.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Solís-Lemus C, Knowles LL, Ané C.
Bayesian species delimitation combining multiple genes and traits in a unified framework.
Evolution. 2015 Feb;69(2):492-507. doi: 10.1111/evo.12582. Epub 2015 Jan 16. PMID: 25495061.
:: DESCRIPTION
Phyto-PhyloPars web server takes an evolutionary perspective to the variability across phytoplankton taxa in order to estimate the size, maximum growth rate, phosphate affinity and susceptibility to predation of any phytoplankton taxon, based on over one thousand observations on freshwater species.
::DEVELOPER
The Centre for Integrative Bioinformatics VU
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
Bruggeman, J. (2011)
A phylogenetic approach to the estimation of phytoplankton traits.
Journal of Phycology 47(1): 52-65.
:: DESCRIPTION
MTDFREML is aset of programs for estimation of genetic (co)variances using multiple-trait derivative-free restricted maximum likelihood
::DEVELOPER
Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
J Anim Sci. 1996 Nov;74(11):2586-97.
Multiple-trait Gibbs sampler for animal models: flexible programs for Bayesian and likelihood-based (co)variance component inference.
Van Tassell CP1, Van Vleck LD.
:: DESCRIPTION
BaTS (Bayesian Tip-Significance testing) is a package that allows the user to test for significant phylogeny-trait correlations whilst taking into account uncertainty arising from phylogenetic error, by integrating over the credible set of topologies produced by Bayesian phylogenetics programs such as BEAST or MrBayes. Null distributions are generated for statistics of phylogeny-trait association, and used to test the significance of the observed data. BaTS can also perform batch analyses of multiple data sets.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Parker J, Rambaut A, Pybus OG. 2008.
Correlating viral phenotypes with phylogeny: accounting for phylogenetic uncertainty.
Infection, Genetics and Evolution 8:239-46
:: DESCRIPTION
aSPU is an R package for adaptive sum of powered score test(ASPU) in genetic association studies.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Adaptive Gene- and Pathway-Trait Association Testing with GWAS Summary Statistics.
Kwak IY, Pan W.
Bioinformatics. 2015 Dec 10. pii: btv719.
:: DESCRIPTION
KMgene is an unified R package for gene-based association analysis for complex traits
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: MORE INFORMATION
Citation
Yan Q, Fang Z, Chen W.
KMgene: a unified R package for gene-based association analysis for complex traits.
Bioinformatics. 2018 Jun 15;34(12):2144-2146. doi: 10.1093/bioinformatics/bty066. PMID: 29438558; PMCID: PMC6246171.
:: DESCRIPTION
PrediXcan is a gene-based association test that prioritizes genes that are likely to be causal for the phenotype.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Gamazon ER, Wheeler HE, Shah KP, Mozaffari SV, Aquino-Michaels K, Carroll RJ, Eyler AE, Denny JC; GTEx Consortium, Nicolae DL, Cox NJ, Im HK.
A gene-based association method for mapping traits using reference transcriptome data.
Nat Genet. 2015 Sep;47(9):1091-8. doi: 10.1038/ng.3367. Epub 2015 Aug 10. PMID: 26258848; PMCID: PMC4552594.
:: DESCRIPTION
iCTNet (integrated Complex Traits Network) is a large-scale network, assembling human disease-gene association, tissue-gene association, disease-tissue associations, protein-DNA interactions, protein-protein interactions and drug-target information.
::DEVELOPER
:: SCREENSHOTS
N/A
::REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
BMC Bioinformatics. 2011 Sep 26;12:380. doi: 10.1186/1471-2105-12-380.
iCTNet: a Cytoscape plugin to produce and analyze integrative complex traits networks.
Wang L1, Khankhanian P, Baranzini SE, Mousavi P.
:: DESCRIPTION
traseR performs GWAS trait-associated SNP enrichment analyses in genomic intervals using different hypothesis testing approaches, also provides various functionalities to explore and visualize the results.
::DEVELOPER
li chen<li.chen at emory.edu>
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
traseR: an R package for performing trait-associated SNP enrichment analysis in genomic intervals.
Chen L, Qin Z.
Bioinformatics. 2015 Dec 18. pii: btv741.
:: DESCRIPTION
TM (Threshold Model) is a (Fortran90) software for multiple trait estimation of variance components, breeding values and fixed effects in threshold, linear and censored linear models in animal breeding. As of August, 2011 it has been modified to accept random seeds on input, and also to include user-defined covariance matrices among individuals (for instance, genomic relationship matrices).
::DEVELOPER
Andrés Legarra , andres dot legarra at toulouse point inra punto fr
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION