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.
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.
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.
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.
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.
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.
Optimizes selection, maintenance of genetic diversity, and mate allocation in breeding programs. AlphaMate’s goal is to find a valid mating plan that delivers desired targets. It enables both animal and plant breeding programs to be more optimal and aims to simplify new research opportunities. This tool can be applied in two cases: (1) maximizing efficiency of converting genetic diversity into genetic gain in a rapid recurrent genomic selection program for wheat; and (2) expanding the gain-diversity frontier with genome editing.
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.
Estimates the parameters of stochastic metapopulation models for the within–host dynamics of infection. SPEEDI.R is a functional and flexible computational framework that estimates the bacterial division and death rates within each organ, and migration rates between each pair of compartments. It also permits to track the probability distribution of the number of copies of a tagged strain of bacteria across a network of anatomical compartments within an animal.
Consists in an unsupervised network-based classification method. This algorithm allows users to perform echolocation click classification, and it considers a set of clicks as a group of objects that are similar but not identical to one another. Clicks can be represented by nodes and the lines or edges between nodes.
Determines pathogenicity in a population based on a state dependent model and trinucleotide repeat sequences (TRS)-polymerase chain reaction (PCR) profiling. ppbEcoli is useful to researchers as it seems that biological studies can require restricted BiSSE setups. This tool was evaluated by comparing the observed fractions of pathogenic strains to the composite parameter.
Determines missing race and ethnicity information in electronic medical record (EMR) datasets. RIDDLE is based on a multilayer perceptron (MLP) and on a deep neural network architecture that can conduct a systematic evaluation of racial and ethnic patterns for approximately 15 000 different medical events. It is useful for race and ethnicity imputation in anonymized EMR datasets.
Integrates and visualizes disease-associated Chromosomal rearrangement (CR) events and chromosomal 3D structure. 3Disease Browser generates a new page with detailed topologically associated domains (TAD) and 3D model information for each gene name or disease name typed in the search panel. The user can interactively rotate and zoom the 3D structure, and click different ChIP-seq data buttons to view the corresponding epigenetic information overlaid on the 3D structure.
Avoids the risk of false positive in detection of genomic regions in current population genetics. HacDivSel detects divergent selection from populations connected by migration. It is based on two methods: one combines haplotype information with inter-population differentiation and the other independently segregates markers. The tool appears to be useful for detecting locally adapted polymorphisms. It works well even when the phasing accuracy is not perfect.
Provides functions to i) encode existing species occurrence datasets and checklists, such as records from natural history collections or observations, in the Darwin Core standard to enhance interoperability of data, and ii) publish and archive data and metadata for broad use in a Darwin Core Archive, a set of files following a standard format. DOIs and citations can be automatically generated for datasets in a standard format; a new DOI can be assigned to a dataset each time it undergoes scientifically significant changes and a version history is kept for each dataset, allowing researchers to easily track changes all previous versions. The guiding design principles of the IPT were to support how data publishers actually use their own databases, and to facilitate the public sharing of datasets with the fewest possible obstacles.
A simple and versatile homemade tool, for the real-time systematic automated surveillance of IDs at Marseille university hospitals, based on the data from our clinical microbiology laboratory, including clinical samples, tests and diagnoses. EPIMIC was specifically designed to detect abnormal events as IDs are rarely predicted and modeled. An abnormal event corresponds to an increase above, or a decrease below threshold values calculated based on the mean of historical data plus or minus 2 standard deviations, respectively. EPIMIC proved to be efficient for real-time automated laboratory-based surveillance and alerting at our university hospital clinical microbiology laboratory-scale.
Assists users in optimizing the impact of combinations of interventions for the control and elimination of malaria transmission. VCOM is a modeling framework that describes the population dynamics of mosquito vectors for prediction of the impact of combined vector control interventions. The software can be useful in selecting interventions for vector control trials and operational research, and in the design of trials themselves. Advanced options are available to alter the parameter values of the mosquito ecology and intervention models.
Provides a platform allowing users to interact with a species-habitat model for ring-necked pheasant (Phasianus colchicus) encompassing at a spatial scale to on-the-ground. Pheasant Habitat Simulator transposes a statistical model of pheasant-habitat relationships in Nebraska into visualizations. The program is available as both a web application and a standalone software which permits to accommodate a wide array of statistical models and conservation challenges.
Aims to analyze diverse protein populations. ScaffoldSeq assists in characterizing the single site and pairwise amino acid frequencies across the population. This tool supplies method for quantifying and removing background cluster similar protein families, sequences, and dampen the impact of dominant clones. It can furnish graphical and tabular summaries for each region of interest, simplifying evaluation of the diversity in a site-specific manner.
Manages and prepares data exploited into genetic epidemiology and population genetics analysis. DIVERGENOME is a platform that consists of two main panels: (i) DIVERGENOMEdb supplies a utility to store and link contigs, single nucleotide polymorphisms (SNPs)/INDELs and microsatellites; and (ii) DIVERGENOMEtools furnishes an assortment of conversion tools which can generate files supported by 10 different software programs including PHASE, Haploview or SWEEP.
Allows estimation of individual breed composition using a Bayesian approach. BIBI is a statistical model that permits to obtain point and interval estimates of breed composition and to make useful probabilistic statements about it. It was implemented with real data using a multibreed beef cattle population from the University of Florida’s Beef Research Unit (BRU).
Assists in estimating population recombination rate based on intraspecific DNA polymorphism data. FastEPRR allows users to create genetic maps and to study recombination hotspots in the genomic era. It can be supported by computer clusters and is suitable for the analysis of population genomic data even when sample sizes are large. Moreover, it can handle the missing data often encountered in genomic scale population data sets.
Constructs plausible ancestral recombination graphs (ARGs) for whole genomes of thousands of sequences. ARG4WG does not only lead to fewer recombination events but also keeps the number of internal nodes stable after the recombination events. It reduces the computational cost significantly in searching for the longest shared segments. This method can handle thousands of samples across whole chromosomes in a single run in an acceptable running time.
Uses haplotypes derived from existing phased marker array genotypes to identify which individuals should be sequenced. AlphaSeqOpt is a heuristic method for allocating low-coverage sequencing resources. This method is extended with an approach to filter out rare haplotypes. It has two main steps: (i) the initial set selection, where an initial set of individuals is selected by iteratively choosing the individuals that are the most complementary to the ones already in the set according to a score function and (ii) the set refinement, where the initial set of individuals is refined through several rounds of exchanges.
Creates neutral landscape models (NLMs). NLMR simplifies a reproducible workflow while being distinct from the naming conventions of other geospatial software. It is useful in all landscape analyses in which one wants to test the influence of NLMs on ecological dynamics. This tool can serve to study disease persistence in heterogeneous landscapes or to determine bias resulting from increased scaling of landscape patterns.
Summarizes personal genotypes, yielding 'genotype fingerprints' that can be readily compared to estimate relatedness. Genotype Fingerprints is based on locality-sensitive hashing. It computes ‘fingerprints’ of genome-wide single nucleotide polymorphism (SNP) array genotypes as reported by directly to consumers (DTC) genetics companies. This tool can be useful to recognize genotypes from the same individual, from closely related individuals, or from a known population, and to cluster individuals into sub-populations de novo.
Allows development of classified maps of land cover at Landsat spatial resolutions. REMAP is based on the geospatial data storage and analysis capacity of the Google Earth Engine. It aims to support the global effort to assess the status of all ecosystem types on earth. This tool can sort land cover according to user-supplied training data and a set of globally available remote sensing datasets as predictor variables.
Allows research on ecosystem functions in real and dynamic natural landscapes. fluxweb offers tools for research on quantitative food webs and ecosystem functions to examine network stability that are important in the face of global changes and species loss. It uses several input parameters that define energetic losses. The software provides a flexible quantitative framework that can be useful to test ecological hypotheses associated to fluxes in networks.
Computerizes historical land-use maps. HistMapR includes several functions to process digitization of historical land-use maps in a R environment. This software provides image smoothing, assignment of user-defined colors, testing of classification and writing to raster file. It minimizes potential sources of error according to the historical map by tailoring classification to fit a specific research.
Enables to forecast rodent abundances and evaluate predictions on a monthly basis. Portal Forecast consists of an iterative near-term forecasting pipeline. It supports the six stages of converting raw data into new forecasts: data collection, data sharing, data manipulation, modeling and forecasting, archiving, and presentation of the forecasts. This tool is useful to develop short-term ecological forecasting systems.
Allows users to study the development of communities of organisms that compete for steadily supplied resources. ITEEM is a simple, intuitive eco-evolutionary model at the interaction level, and with a life-history trade-off between interaction traits and replication rate. The model reproduces in a single framework several phenomena of eco-evolutionary dynamics. It allows detailed analysis of mechanisms and can guide experimental tests.
Indexes paths of graphs including haplotype-level information. CHOP is a standalone software able to deconstruct a graph to generate a set of linear sequences. The application proposes an haplotyping constraint to facilitate graph alignment scalability and long paths indexation which intends to assist users in exploiting population graphs for sequencing analysis. It can be used for substring queries on the paths that span across nodes and edges of the graph.
Computes tasks involved in most landscape investigation. Landscapetools provides visualization, classification and merging methods. It eases the utilization of factorial encoding of landscape data in a raster object. This tool is useful for the finding of disease persistence in heterogeneous landscapes or for the estimation of bias resulting from increased scaling of landscape patterns.
Formalizes causal relationships between somatic genomic events, signaling pathway activity and immune activity in the tumor. CMIF infers directed interactions between signaling pathway activity and immune activity by anchoring the analysis on somatic genomic changes. The software was used to propose 11 novel genomic drivers of T cell phenotypes in the breast cancer tumor microenvironment. Analysis was focused on breast cancer, but the methodological framework can easily be applied to many other forms of the disease.
Calculates vegetation phenological cycle and detects anomalies by using remote sensing data. npphen can reconstruct the expected land surface phenology (LSP) for the complete time period of two contrasting ecosystems by exploiting long time series of satellite imagery. This software offers basic and high-level features for manipulating vector data (numerical series) and raster data (satellite derived products).
Allows the study of animal incubation. incR implements a method that exploits variation in incubation and ambient temperature to calculate the presence or absence of the incubating individual in the nest. The software can be used to study incubation in a broad range of species and ecological contexts. It can assist the community of researchers in studying incubation both in the wild and in the laboratory.
Recognizes hydrological regimes of temporary rivers. TREHS can assist users in the understanding of riverine ecosystems and contributes to their sound management. It permits users to operationally monitor, assess and classify the regime of temporary rivers. This tool calculates the degree of hydrological alteration with an expert scoring method from the differences between the metrics obtained for the reference regime and the actual one.