:: DESCRIPTION
Physher is a maximum likelihood-based method for estimating evolutionary rates and divergence times from genetic data.
::DEVELOPER
SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Fourment M, Holmes EC.
Novel non-parametric models to estimate evolutionary rates and divergence times from heterochronous sequence data.
BMC Evol Biol. 2014 Jul 24;14:163. doi: 10.1186/s12862-014-0163-6. PMID: 25055743; PMCID: PMC4222489.
:: DESCRIPTION
pyGenClean is an informatics tool to facilitate and standardize the genetic data clean up pipeline with genotyping array data. In conjuction with a source batch-queuing system, the tool minimizes data manipulation errors, it accelerates the completion of the data clean up process and it provides informative graphics and metrics to guide decision making for statistical analysis.
::DEVELOPER
Marie-Pierre Dubé’s Laboratory
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2013 May 30. [Epub ahead of print]
pyGenClean: efficient tool for genetic data clean up before association testing.
Lemieux Perreault LP, Provost S, Legault MA, Barhdadi A, Dubé MP.
:: DESCRIPTION
AdmixSim is an individual-based forward-time simulation tool that can flexibly and efficiently simulate population genomics data under complex evolutionary scenarios. It is based on the extended Wright-Fisher model, and it implements many common evolutionary parameters to involve gene flow, natural selection, recombination, and mutation.
::DEVELOPER
Population Genomics Group (PGG)
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Zhang R, Liu C, Yuan K, Ni X, Pan Y, Xu S.
AdmixSim 2: a forward-time simulator for modeling complex population admixture.
BMC Bioinformatics. 2021 Oct 18;22(1):506. doi: 10.1186/s12859-021-04415-x. PMID: 34663213; PMCID: PMC8522168.
:: DESCRIPTION
bammds is a software that allows to create a multidimensional scaling (MDS) plot of populations for genetic data.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
bammds: A tool for assessing the ancestry of low depth whole genome data using multidimensional scaling (MDS).
Malaspinas AS, Tange O, Moreno-Mayar JV, Rasmussen M, DeGiorgio M, Wang Y, Valdiosera CE, Politis G, Willerslev E, Nielsen R.
Bioinformatics. 2014 Jun 28. pii: btu410.
:: DESCRIPTION
adegenet is an R package dedicated to the exploratory analysis of genetic data. It implements a set of tools ranging from multivariate methods to spatial genetics and genome-wise SNP data analysis.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Jombart (2008),
“adegenet: a R package for the multivariate analysis of genetic markers“,
Bioinformatics, 24:1403-1405.
:: DESCRIPTION
The pbwt package provides a core implementation and development environment for PBWT (Positional Burrows-Wheeler Transform) methods for storing and computing on genome variation data sets.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2014 May 1;30(9):1266-72. doi: 10.1093/bioinformatics/btu014. Epub 2014 Jan 9.
Efficient haplotype matching and storage using the positional Burrows-Wheeler transform (PBWT).
Durbin R.
:: DESCRIPTION
Genoppi is an open-source software for performing quality control and analyzing quantitative proteomic data. Genoppi streamlines the integration of proteomic data with external datasets such as known protein-protein interactions in published literature, data from genetic studies, gene set annotations, or other user-defined inputs.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Pintacuda G, Lassen FH, Hsu YH, Kim A, Martín JM, Malolepsza E, Lim JK, Fornelos N, Eggan KC, Lage K.
Genoppi is an open-source software for robust and standardized integration of proteomic and genetic data.
Nat Commun. 2021 May 10;12(1):2580. doi: 10.1038/s41467-021-22648-5. PMID: 33972534; PMCID: PMC8110583.
:: DESCRIPTION
SPA is a method for predicting ancestry or where an individual is from using the individual’s DNA. Accurately modeling ancestry is an important step in identifying genetic variation involved in disease.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Wen-Yun Yang, John Novembre, Eleazar Eskin and Eran Halperin.
A model based approach for analysis of spatial structure in genetic data.
Nature Genetics, 44, 725–731 (2012).
:: DESCRIPTION
FastPop is an efficient R package that fills the gap between Structure and Eigenstrat. It can: 1, generate PCA scores that identify ancestral origins and can be used for multiple studies; 2, infer ancestry information for data arising from two or more intercontinental origins.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
FastPop: a rapid principal component derived method to infer intercontinental ancestry using genetic data.
Li Y, Byun J, Cai G, Xiao X, Han Y, Cornelis O, Dinulos JE, Dennis J, Easton D, Gorlov I, Seldin MF, Amos CI.
BMC Bioinformatics. 2016 Mar 9;17(1):122. doi: 10.1186/s12859-016-0965-1.
:: DESCRIPTION
pong is a freely available software package for post-processing output from clustering inference using population genetic data
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
pong: fast analysis and visualization of latent clusters in population genetic data.
Behr AA, Liu KZ, Liu-Fang G, Nakka P, Ramachandran S.
Bioinformatics. 2016 Jun 9. pii: btw327.
