Crowdsources genomic and phenotypic information for human genetics research. DNA.Land aims to show the potential for genotype and phenotype collection by crowdsourcing data from users of direct-to-consumer (DTC) companies. It provides over 50 000 genomic datasets from DTC participants. This tool employs a hybrid cloud design to collect data in a cost-effective manner. It consists of a digital biobank integrating data from genetic, genealogical, and social media resources.
Permits high throughput, detailed and fully automated prediction of potential binding. iCR is a web server tool, for identification of conserved high priority targets of a regulatory protein from heterologous sequence data of prokaryotes (which includes regulatory sequences of genes and their orthologs in other species). Users can easily distinguish biologically important motifs from background noise based on their cross-species conservation.
Evaluates polymorphism and divergence sites in genomic sequences of multiple species to pinpoint the genes under positive of negative selection. HDMKPRF can detect the occurrence time of selection to a specific lineage of the species phylogeny. This approach exploits population genetics models that use Bayesian Poisson random field framework and fuses information over all gene loci to enhance the detect selection feature.
Performs genome scans with next generation sequencing data. pcadapt is an R package that was developed to detect genes under selection based on population genomic data. It assumes that markers excessively related with population structure are candidates for local adaptation. This module can handle missing data as well as pooled sequencing data. It also implements a robust Mahalanobis distance as a test statistic.
Analyzes next-generation DNA sequence data with or without a genetic map. bgc is a software that uses Markov chain Monte Carlo (MCMC) to generate samples from the joint posterior probability distribution of the parameters. This software is suitable for analysis of large sequence data sets with uncertainty in genotype due to sequence errors or finite sequence coverage. It was developed to facilitate population genomics research.
Facilitates analysis of single nucleotide polymorphism (SNP) data. dartR is designed as a workhorse for the preparation of SNP datasets for population genomics and phylogenomics, for the exploration of the data, and the production of framework analyses common in these types of analyses. The software provides more than 20 new filtering functions to subset SNP data. It uses the genlight data format, a single standard format permitting an efficient data processing workflow.
Automates breeding group selection for founding breeding programs. Swinger is a computer program designed to be highly flexible, with the user able to decide the number and sex composition of breeding groups and the allowable level of internal and pairwise relatedness given the available resources for captive breeding and the biology of the species. It has a user-friendly graphic interface and input parameters that are highly flexible to the reproductive system of the target system and the biotic and abiotic resources available for captive breeding.
Handles multivariate and sample locality information analysis in geographic space. mvMapper offers an interface for exploring statistical framework in ordination and geographical space. The software is composed of a statistical panel, a mapping panel - both interactive with tools for panning, zooming in and out, and saving, and a metadata panel for allowing a rapid exploration of metadata with regard to population structure.
Allows users to estimate the population size parameter θ from genomic data. The ThetaMater method assists users in detecting bounds of mutation counts from the posterior distribution. It permits users to filter out loci with high mutation counts representing spurious loci.
Supports the identification of therapeutically actionable genomic alterations in tumors. CGI (i) identifies validated oncogenic alterations in a tumor, (ii) predicts the effect of the remaining alterations of uncertain significance, (iii) reports the known influence of these variants on drug response according to the level of clinical evidence supporting it and (iv) lists the interactions of existing chemical compounds with genes bearing driver alterations.
Gives access to the Lake Multi-scaled Geospatial and Temporal (LAGOS-NE) database. LAGOSNE is an R package that aims to provide an easier access to the complete dataset and its documentation. The application allows users to retrieve, store, and interact with the records compiled about 50 000 lakes and reservoirs in 17 US states. It includes functionalities for accessing to information relative to lake water quality and ecological context data.
Provides a graphical user interface (GUI) for the latest Isolation with Migration (IM) program. IMGui provides a comprehensive set of tools for performing demographic analyses, tracking progress of runs, and visualizing results. It is developed using node. js and the Electron framework. IMGui can be used across operating systems and platforms, allows interactive validation and monitoring of runs, produces trace-plots and histograms of run parameters at regular intervals, and assists with mining run outputs to create publication quality graphs and visualizations.
Aims to determine a number of genetic parameters from mapped shotgun data obtained from diploid individuals. mlRho is based on maximum likelihood estimators for θ and sequencing error. It can serve for the estimation of the rate of recombination from the correlation between the zygosity at pairs of nucleotide positions. This tool allows users to customize parameters such as average read length, coverage and error rate.
Determines if a genomic window has experienced gene flow between two related populations and their direction. FILET proceeds by leveraging population genomic data from these populations. This software uses deep learning methods and works by combining information from several population genetic summary statistics that keep patterns of variation across these two populations. It assigns a genomic window according to three classes: introgression from population 1 into population 2, introgression from population 2 into population 1, and the absence of introgression.
Allows users to generate alleles. GetCrosses selects one allele for each locus from each parent to generate the alleles of a new individual and simulates offspring genotypes from a single-nucleotide polymorphism (SNP) file for their use in relatedness analysis. This tool is useful for researchers wishing to realize simulations for different pedigree and estimate the relatedness values for all relationships within the artificial pedigree.
Provides a platform for reproducible modeling of species niches and distributions. Wallace is an open-source application that offers user-friendly access to R-scripted modern workflows. The given correlative models estimate the response of a species to the environment. It can be used to infer (or hypothesize) geographic ranges, environmental suitability across a landscape, or niche requirements.
Assesses and ranks Integrated Crop Management (ICM) strategies. SIPPOM-WOSR is a simulator for integrated pathogen population management. It is a model that links epidemiological, population and crop model approaches, simulating both quantitative (size) and qualitative evolution (genetic structure) of the L. maculans population. It is useful for designing and assessing cropping systems that seek to control phoma stem canker while both preserving the efficacy of specific resistance and meeting requirements of ICM.
Provides a method for computing spread of infections. Model for communicable disease outbreak dynamics provides a repository composed of a simulator coupled to an Engine for Likelihood-free model. The application is based on the birth-death (BD) process which aims to improve the identifiability issues and estimation of the underlying infectious population size estimation. It was tested on epidemiological data collected about tuberculosis (TB) in the San Francisco Bay area.
Estimates complexity of infection and population allele frequencies using single nucleotide polymorphism (SNP) data obtained from Sequenom or similar types of SNP assays. THE REAL McCOIL is a Markov chain Monte Carlo (MCMC) method that facilitates population genetic analysis when there are polygenomic infections, which are common in many malaria endemic areas. It provides a robust tool for understanding the molecular epidemiology of malaria across transmission settings.
Incorporates characteristics of human innovation and offers an explanation for one of the puzzling observations in the archaeological record of stone tools: its extreme punctuation. GameChangingInnovations encompasses two realistic ways in which innovations can affect the trajectory of cultural evolution: one in which a large-scale innovation, for example a more effective subsistence strategy, can alter the population size and thus the cultural steady state of the population, and one in which a large-scale innovation, such as writing or other mechanisms of preserving cultural information, can affect the rate of cultural loss. With all external factors remaining constant, a population’s cultural gains and losses reach an eventual cultural steady state, such that the rates of cultural innovation and loss balance one another and the population maintains a relatively stable number of tools.