Allows users to perform population-based association studies. SFPCA can be applied to various types of genetic data and several types of family or unrelated-individual data. The software aims to enrich for rare risk or for protective variants by furnishing a way to include families in association studies. It was experimented on two datasets.
Handles family data with a pedigree object. Pedigree plotting features have been updated to display features on complex pedigrees while adhering to pedigree plotting standards. Kinship matrices can now be calculated for the X chromosome. Other methods have been added to subset and trim pedigrees while maintaining the pedigree structure.
A pedigree-drawing application with special features for easy visualization of complex haplotype information. HaploPainter has been developed to facilitate gene mapping in mendelian diseases in terms of fast and reliable definition of the smallest critical interval harbouring the underlying gene defect. Features like haplotype compression and the ability of marker section cut-out are particularly helpful for viewing large SNP-derived haplotypes.
Allows users to handle large and complex pedigrees with an emphasis on readability and aesthetics. Madeline includes a desktop version and a web version permitting researchers to create, display, save and print pedigrees. Moreover, it can convert pedigree and marker data into various formats required by linkage analysis software and also supply functionality for querying pedigree data sets interactively.
A Java API for the visual analysis of large and complex pedigrees. PedVizApi provides all the necessary functionality for the interactive exploration of extended genealogies. While available packages are mostly focused on a static representation or cannot be added to an existing application, PedVizApi is a highly flexible open source library for the efficient construction of visual-based applications for the analysis of family data.
Graphically displays genealogical data in 3D. Celestial3D employs specifically developed visualization techniques including layout algorithms that avoid screen clutter, and shadows that demarcate clades, so that extensive pedigrees are readily interpretable. The software allows to display multiple families in a unique spiral view. Use of 3D allows a greater number of individuals to be displayed in a given area, closely related individuals to be displayed spatially near each other and improved focus and context techniques.
Allows haplotype visualization and pedigree drawing. HaploForge is a comprehensive web application that draws pedigrees with a simple drag and drop interface and displays haplotypes underneath each individual, allowing for side-by side comparison, irrespective of generation. Drawn pedigrees are compliant with the Pedigree Standardization Work Group (PSWG) specification. The software is specifically designed for navigating high numbers of markers.
Provides a multi-criteria approach for monitoring endangered breeds based on subjective thresholds of a government agency. The GenMon application integrates different types of criteria, as pedigree data, genetic introgression, socio-economic and environmental aspects and geographical concentration of the breeds. This tool computes a global sustainability index for each breed, and making it possible to compare the endangerment level of several species and breeds.
Allows to visualize pedigree. Helium allows users to easily integrate a number of data types along with large plant pedigrees to offer an integrated environment in which they can explore pedigree data. It takes a string of genotypic data and identifies possible matches from data held in our Germinate database then display the possible hits on the pedigree display. The tool models pedigree as graph nodes to represent plant lines and edges to show mating/parentage.
Includes basic functions to manage genealogical data allowing, for example, extraction of a part of a genealogy or selection of specific individuals. There are also many functions providing information to describe the size and complexity of genealogies as well as functions to compute standard measures such as kinship, inbreeding and genetic contribution. GENLIB also includes functions for gene-dropping simulations. It provides a user friendly and flexible environment to analyze extensive genealogical data, allowing an efficient and easy integration of different types of data, analytical methods and additional developments and making this tool ideal for genealogical analysis.
Assists users in the production of a pedigree chart. f-treeGC allows users to edit a pedigree chart to visualize the larger chart with multiple displays. The users may select “Add comment,” right-click on the comment box, and then type the appropriate text. In summary, its interface enables users without specialized knowledge of clinical genetics and graphical skills to easily create medical pedigrees.
Is the intelligent pedigree drawing tool that's designed to work the way you think. Cyrillic is a powerful program that brings together all the tools you need for drawing family pedigrees, and managing and analyzing pedigree data.
Draws large, complex pedigrees containing inbred loops and multiple-mate families. PedigreeQuery is based on a step-by-step approach to imaging, when the researcher determines the direction of further extension of the scheme. The software package permits constructing not only whole pedigrees, but also their fragments that are particularly interesting for research. PedigreeQuery also allows for adding new information on the phenotypes and genotypes of pedigree members.
Permits to visualize multivariate trees and tree-like graphs using a linearization approach. Lineage supports domain experts that study such multifactorial diseases in the context of genealogies. It is able to scale multiple families with hundreds of members across several generations. The tool can incorporate extensive, multivariate attributes in the analysis of the genealogy without cluttering the graph. It can be generalized to other scenarios.
Investigates pedigrees with millions of individuals. SciLMM consists in the idea that pedigree data can be encoded in a sparse manner. It implements approaches for linear mixed models (LMM) analysis in the presence of the dependencies encoded by matrices constructed by the model. This tool is flexible and can be extended in various directions. It is useful for genome wide association studies (GWAS).
Is able to draw pedigrees with complex inbreeding structures over multiple generations in a population with a large number of individuals, as is common in animal populations. Options include: full pedigree, summarization, extraction of individual pedigrees, inbreeding calculation, coancestry coefficient calculation, color control, drawing size, page size and margins, drawing styles.
Calls Graphviz dot to draw pedigrees. PedVis takes a data frame that lists a pedigree in three columns (kid, pa, ma) and make a .dot file for a marriage node diagram of the thing. It draws simple pedigree as a marriage node diagram and puts labels on everyone and makes some of the p-node factors invisible.
Calculates probabilities of gene origin, relationship and inbreeding coefficient. PEDIG works about the pedigree information: (1) it manipulates, extracts and encodes the pedigree information; (2) it searches pedigree errors and common ancestors; (3) it analyses pedigree information and informs about it quality.
Assists in creating pedigree diagrams. Genial Pedigree Draw creates charts in real time. It permits to view the family history and inheritance patterns as the pedigree grows. It can also export diagrams in PNG or SVG and import data from other design tools. An online solution and a local solution are available. These diagrams were developed to be used for both clinical use, in an educational environment and also to create animal pedigree trees.
An open source graph visualization software. The Graphviz layout programs take descriptions of graphs in a simple text language, and make diagrams in useful formats, such as images and SVG for web pages; PDF or Postscript for inclusion in other documents; or display in an interactive graph browser. Graphviz has many useful features for concrete diagrams, such as options for colors, fonts, tabular node layouts, line styles, hyperlinks, and custom shapes.
Allows users to discover blocks of identity throughout a pedigree. ISCA is a standalone software, based on a hidden Markov model (HMM), which is suited for the analysis of whole-genome data without the need of phased data or population controls. The program can also detect both IBD1 and IBD2 segments between pairs of individuals with an unknown relationship assisted by a feature that permits the removal of noise from segments of the genome.
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