Search Results for "genetics"
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Showing 51 open source projects for "genetics"
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Amazon Genomics CLI
Tool to simplify the processes of deploying the AWS infrastructure
... infrastructure, providing you with an easy-to-use command-line interface to quickly setup and run genomics workflows on Amazon Web Services (AWS) specified by languages like WDL. By removing the heavy lifting from setting up and running genomics workflows in the cloud, software developers and researchers can automatically provision, configure and scale cloud resources to enable faster and more cost-effective population-level genetics studies, drug discovery cycles, and more. -
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123VCF
An Intuitive and Efficient Tool for VCF file filtration
... Bioinformatics 25, 68 (2024). https://doi.org/10.1186/s12859-024-05661-5 _____________________________________ Authors: Milad Eidi, Samaneh Abdolalizadeh, Soheila Moeini Supervisors: Javad Zahiri, PhD - Masoud Garshasbi, PhD Department of Neuroscience, University of California San Diego, California, USA Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran -
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Nemo
Individual-based forward-time genetics simulation software
Nemo is an individual-based, forward-time, genetically explicit, and stochastic simulation software designed for the study of the evolution of life history and quantitative traits, and genetic markers under various types of selection, in a spatially explicit, metapopulation framework. -
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Mendel’s Accountant is a biologically realistic, forward-time, parallel, numerical simulation program which models genetic change within a population, as affected by mutation and selection.
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est-sfs
Estimate the unfolded site frequency spectrum and ancestral states
.... For details of the method, see Keightley and Jackson, Genetics 209: 897-906 (2018). -
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coatli
Second and third moments of the "Site frequency spectrum".
In population genetics, the "site frequency spectrum" is an important summary statistic of the variation in aligned DNA sequences. This package contains implemented algorithms for the analytical calculation of the expected second and third moments of this spectrum (under the standard neutral Wright-Fisher model). Furthermore there are utilities to estimate these quantities from coalescent simulation (using output of the program 'ms', written by R.R. Hudson). As an add-on some small utilities... -
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Jack LIRE (Linked Record)
Quantum universal object system with referencing and genetics
Jack LIRE (Linked Record) is a quantum database-backed life-long text record diary with referencing (linking) between records, and a data library for life-long keeping of files such as documents, photographs, music and more. The diary records are fully searchable. Files can be mentioned in diary records to preserve memories, document knowledge and ideas, and more. Massive numbers of diary records and files can be permanently kept. A database located on one computer can be accessed from... -
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SVPhylA
SVPhylA: Sequence Vectorization for Phylogenetic Analyses
...-Kernel (non-lineal). In addition, genetic distances derived can be either combined between them or with the alignment-free distances. So far, SVPhylA contain a module to compare tree topologies by using different distance measures as a validation procedure. The statistical validation (bootstrap and jacknife) of the alignment-free trees is being developed SVPhylA is mostly designed to interact to MEGA (MOLECULAR EVOLUTIONARY GENETICS ANALYSIS). -
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fcGENE: Genotype format converter
Format converting tool for genotype Data (e.g.PLINK-MACH,MACH-PLINK)
Main application is twofold: first to convert genotype SNP data into formats of different imputation tools like PLINK MACH, IMPUTE, BEAGLE and BIMBBAM, second to transform imputed data into different file formats like PLINK, HAPLOVIEW, EIGENSOFT and SNPTEST. Readable file formats: plink-pedigree (ped and map), plink-raw, plink-dosage, mach , minimac, impute, snptest, beagle and bimbam. Similarly all kinds of imputation of outputs are also accepted. Formats which can be generated by... -
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LiveGMS is a PHP/MySQL driven gene editor for the game Creatures 3 / Docking Station. It provides a platform independent online editor with most features other binary genetics editors have.
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EggLib
Evolutionary Genetics and Genomics Library
EggLib has moved to http://mycor.nancy.inra.fr/egglib/ since version 3.0.0. -
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Application to estimate haplotypes and other genetics data, based on maximum likehood approach. It can handle present-absent as well as multiallelic loci.
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Forward Simulation
A Wright-Fisher forward population genetics simulation.
The forward simulation code is a tool to model evolution of a population under the Wright-Fisher model. The code incorporates population expansion, bottleneck, speciation and migration. Several selection and fitness mechanisms are available: selective sweeps, foreground selection in one region with a distinct background selection in neighboring regions, epistasis, and truncation selection. The code is implemented in the C++ programming language. -
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SMARTPOP
Fast forward-in-time simulation software for population genetics
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SysGenSIM is a bioinformatics toolbox to create artificial gene expression datasets by simulating Systems Genetics experiments.
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CCH
A genetics tool that identifies genomic regions of shared ancestry
Combinatorial Conflicting Homozygosity (CCH) uses dense Single Nucleotide Polymorphism (SNP) genotypes to identify regions of the genome inherited from a common ancestor among any or all subsets of a group. Analysis is rapid and can identify loci containing genes for dominant traits. CCH is robust to the presence of phenocopies and can detect undisclosed shared common ancestry. The associated publication regarding CCH may be accessed here: http://www.biomedcentral.com/1471-2164/16/163 If... -
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MERAP
Medical Resequencing Analysis Pipeline
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Athus
Manage, merge, filter and convert population genetics data
This project assists you in performing population genetic analyses by taking over the ugly, boring and error-prone data manipulation steps. Starting from well specified input formats VCF, BED and FASTA and a unique configuration file describing data (f.e. from SNP-arrays or sequencing) as well as filtering one can create standard POPGEN formats like Eigenstrat, PEDMAP (PLINK), Treemix ... In addition there are several utilities for * generating VCF from SNPArray data (NCBI - GEO, Illumina... -
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coalescent
Software tool for Research in Computational Population Genetics
Development of exact and approximate methods (Importance Sampling and MCMC based) for computing likelihoods under the standard population genetic models of mutation,migration & recombination. Project issues are mainatined at https://freecode4susant.atlassian.net/browse/COALESCENT -
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VariantMaster
Extract causative variants for monogenic and sporadic genetic diseases
There is a fast growing interest in clinical genetics to the utilization of High Throughput Sequencing data for accurate diagnosis of monogenic diseases. To improve the identification of the variants from HTS, we developed VariantMaster, an original program that accurately and efficiently extracts causative variants in familial and sporadic genetic diseases. The algorithm takes into account predicted variants (SNPs and indels) in affected individuals or tumor samples and utilizes the row (BAM... -
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niGA
Heterogenous Multiprocessor Scheduling Using Genetic Algorithms
Implementation of task scheduling using Genetics algorithm for heterogeneous parallel programming -
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CDPOPgui
GUI Frontend for CDPOP
CDPOPgui is a GUI Frontend for CDPOP What is CDPOP? CDPOP (Cost Distance POPulations) is a spatially-explicit simulator of gene-flow in complex landscapes to explain observed population responses and provide a foundation for landscape genetics. The program implements individual-based population modeling with Mendelian inheritance on a resistant landscape. Simulation begins with an initial homogeneous population and followed by divergence through time as functions of individual based... -
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GenSim
A free chicken genetics simulator
Gensim is a free Mendelian genetics simulator based on the expression of genes in chickens. -
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OpenAIL
Open Artificial Intelligence Library
[Open Artificial Intelligence Library]. This library main goal is to provide a tool box to those who want to use algorithm such as neural network or genetics Algorithm and all algorithms that are commonly within the Artificial Intelligence field.
