Search Results for "genetic"
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Showing 721 open source projects for "genetic"
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1
Genetic algorithm for EOM
A python GA code for EOM in SAXS/WAXS
Because GAjoe of ATSAS cannot deal with WAXS range, and no parameters can be modified. I made a code by myself to use GA for finding best EOM for SAXS/WAXS. The project need ATSAS crysol and a folder with multiple pdb files to use. -
2
Alphafold
Open source code for AlphaFold
... a slightly simplified version of AlphaFold with this Colab notebook or community-supported versions. The total download size for the full databases is around 415 GB and the total size when unzipped is 2.2 TB. Please make sure you have a large enough hard drive space, bandwidth and time to download. We recommend using an SSD for better genetic search performance. -
3
PyGAD
Source code of PyGAD, Python 3 library for building genetic algorithms
PyGAD is an open-source easy-to-use Python 3 library for building the genetic algorithm and optimizing machine learning algorithms. It supports Keras and PyTorch. PyGAD supports optimizing both single-objective and multi-objective problems. PyGAD supports different types of crossover, mutation, and parent selection. PyGAD allows different types of problems to be optimized using the genetic algorithm by customizing the fitness function. -
4
GeneticSharp
GeneticSharp is a fast, extensible, multi-platform and multithreading
GeneticSharp is a fast, extensible, multi-platform and multithreading C# Genetic Algorithm library that simplifies the development of applications using Genetic Algorithms (GAs). Can be used in any kind of .NET 6, .NET Standard and .NET Framework apps, like ASP .NET MVC, ASP .NET Core, Blazor, Web Forms, UWP, Windows Forms, GTK#, Xamarin, MAUI and Unity3D games. GeneticSharp and extensions (TSP, AutoConfig, Bitmap equality, Equality equation, Equation solver, Function builder, etc). A Blazor... -
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5
pydna
Clone with Python! Data structures for double stranded DNA
Clone with Python! Data structures for double stranded DNA & simulation of homologous recombination, Gibson assembly, cut & paste cloning. Planning genetic constructs with many parts and assembly steps, such as recombinant metabolic pathways, are often difficult to properly document as is evident from the poor state of documentation in the scientific literature. The pydna python package provide a human-readable formal description of cloning and genetic assembly strategies in Python which allow... -
6
DeepVariant
DeepVariant is an analysis pipeline that uses a deep neural networks
DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data. DeepVariant is a deep learning-based variant caller that takes aligned reads (in BAM or CRAM format), produces pileup image tensors from them, classifies each tensor using a convolutional neural network, and finally reports the results in a standard VCF or gVCF file. DeepTrio is a deep learning-based trio variant caller built on top of DeepVariant. DeepTrio... -
7
Smile
Statistical machine intelligence and learning engine
Smile is a fast and comprehensive machine learning engine. With advanced data structures and algorithms, Smile delivers the state-of-art performance. Compared to this third-party benchmark, Smile outperforms R, Python, Spark, H2O, xgboost significantly. Smile is a couple of times faster than the closest competitor. The memory usage is also very efficient. If we can train advanced machine learning models on a PC, why buy a cluster? Write applications quickly in Java, Scala, or any JVM... -
8
gplearn
Genetic Programming in Python, with a scikit-learn inspired API
gplearn implements Genetic Programming in Python, with a scikit-learn-inspired and compatible API. While Genetic Programming (GP) can be used to perform a very wide variety of tasks, gplearn is purposefully constrained to solving symbolic regression problems. This is motivated by the scikit-learn ethos, of having powerful estimators that are straightforward to implement. Symbolic regression is a machine learning technique that aims to identify an underlying mathematical expression that best... -
9
Evolutionary.jl
Evolutionary & genetic algorithms for Julia
A Julia package for evolutionary & genetic algorithms. The package can be installed with the Julia package manager. -
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10
Java·Applied·Geodesy·3D
Least-Squares Adjustment Software for Geodetic Sciences
JAG3D is no longer developed at source-forge, and has moved to GitHub. Please visit https://github.com/applied-geodesy/jag3d or https://software.applied-geodesy.org to get the latest version. -
11
Motofit co-refines Neutron and X-ray reflectometry data, using the Abeles matrix / Parratt recursion and least squares fitting (Genetic algorithm or Levenberg Marquardt). It works in the IGOR Pro environment (TM Wavemetrics).
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12
Sudoku Maker is a generator for Sudoku number puzzles. It uses a genetic algorithm internally, so it can serve as an introduction to genetic algorithms. The generated Sudokus are usually very hard to solve -- good for getting rid of a Sudoku addiction.
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13
pgapack, the parallel genetic algorithm library is a powerfull genetic algorithm library by D. Levine, Mathematics and Computer Science Division Argonne National Laboratory. The library is written in C. PGAPy wraps this library for use with Python.
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14
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. -
15
sRNAWorkbench
The UEA sRNA Workbench
A suite of tools for analysing small RNA (sRNA) data from Next Generation Sequencing devices. Including expression profiling of known mirco RNA (miRNA), identification of novel miRNA in deep-sequencing data and identification of other interesting landmarks within high-throughput genetic data -
16
This is the official repository for the CUSTOMHyS-Qt software. CUSTOMHyS-Qt is a GUI for the CUSTOMHyS framework, which is an interactive tool for customysing heuristic-based algorithms. The CUSTOMHyS-Qt is written in Python and uses the PyQt5 library for the GUI. Further references about the backend can be found in the CUSTOMHyS repository.
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17
Alcinoe
compoments suite for Delphi
Project description and support moved to : https://github.com/Zeus64/alcinoe However you can use the source you prefer, the SVN here or the GIT on github, both are synchronized (just that GIT don't support large file > 100 mo so some minor files used only as references are missing from GIT) -
18
Evolutionary Computation Framework
C++ framework for application of any type of evolutionary computation.
ECF is a framework intended for application of any type of evolutionary computation (GA/GP, DE, Clonalg, ES, PSO, ABC, GAn, local search...). It offers simplicity for the end-user (parameterless usage, tutorial) and customization for experienced EC practicioners. -
19
GOBU
Gene Browsing Utility
Gene Ontology Browsing Utility (hereinafter, GOBU, pronounced as "go-boo") is a browsing and manipulating tool for Post-Pipeline genetic data, especially useful for data with GO annotations. With help of GOBU, we expect biologists and their cooperating technicians can pay less effort on common programming stuff. At the same time, GOBU provides an Extendable Architecture which guarantees the possibility of 1. Arbitrary Data Description, 2. Data Integration, and 3. Extendable User Interface. -
20
ntx
Neutrality tests using the SNP site frequency spectrum
Tests on "neutrality" are designed to detect systematic deviations from chance patterns in genetic data. This tool computes for a given SNP site frequency spectrum some standard test statistics like Tajima's D, Fay & Wu's H, etc. Additionally, the user may adapt the tests to specific demographies by specifying non-standard first and secondary moments. These can be obtained e.g. from simulations. -
21
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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22
irixjoker-sensing-utils
sensing in IRIX emulator lib
Uses machine learning to compute with genetic programming for emulators. -
23
Gemi
PCR primers / probes design from multiple & degenerate sequences
Gemi can be downloaded from the site (https://sites.google.com/site/haithamsobhy/software). Please, do not hesitate to contact Dr. Haitham Sobhy if you need help. Gemi, an automated, fast, and easy-to-use bioinformatics tool with a user-friendly interface to design primers and probes for polymerase chain reaction (PCR). Gemi accepts multiple aligned and long DNA and RNA sequences with degenerate nucleotide (non-A/C/G/T bases). Gemi can be used for quantitative, real-time and conventional... -
24
BIGSdb
Software for storing and analysing bacterial sequence data
The Bacterial Isolate Genome Sequence Database (BIGSdb) is a scalable, web-accessible database system designed to store and analyse linked phenotypic and genotypic information in a computationally efficient manner. Sequence data can range from single sequence reads to multiple contigs generated by whole genome sequencing technologies. The system incorporates the capacity to define and identify any number of loci and genetic variants at those loci within the stored nucleotide sequences... -
25
MolMarker
Java software to evaluate the results obtained by molecular markers
Journal article to cite: Jahnke, G.; Smidla, J.; Poczai, P. MolMarker: A Simple Tool for DNA Fingerprinting Studies and Polymorphic Information Content Calculation. Diversity 2022, 14, 497. https://doi.org/10.3390/d14060497 Leave a review, please! Your opinion matters! :-) MolMarker is user-friendly software to help evaluate the research results obtained by molecular markers. The software can handle genetic (e.g. SSR) and biochemical (e.g. isozyme) data, can construct similarity matrices...