Search Results for "genetic algorithm software"
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Showing 27 open source projects for "genetic algorithm software"
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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. ... -
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mapska
The Murder Accountability Project's Serial Killer Algorithm
A much improved Linux/Perl implementation of the Murder Accountability Project's Serial Killer Algorithm. This module was tested with the "SHR76_19.csv" available from www.murderdata.org/p/data-docs.html. This module provides functions to prepare the data, upload to a database and view the identified clusters. Download SHR76_19.csv (23/03/2021) - https://www.dropbox.com/s/ye37woe6et05qgs/SHR76_19.csv.zip?dl=1 For information on this algorithm and the Murder Accountability Project... -
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Base62 Encode/Decode Utility
A tool for encoding/decoding to base62
the package chewingum contains two main programs: - base62 - chew They have been implemented in perl. Base62 has been coded in c++ too. chew has been written to shorten long decimal integer numbers into base62 strings. It's not a mere base conversion, because it doesn't use arithmetic inside its logic. In this way it can convert very long numbers into strings quickly, without overflows. For example if I want to share an id using an url, this will make the url shorter. the... -
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MaxBin
An automatic tool for binning metagenomics sequences
MaxBin is a software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm. Users could understand the underlying bins (genomes) of the microbes in their metagenomes by simply providing assembled metagenomic sequences and the reads coverage information or sequencing reads. For users' convenience MaxBin will report genome-related statistics, including estimated completeness, GC content and genome size in the binning summary page. -
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CABBaGe
Classification Algorithm Based on a Bayesian method for Genomics
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MicroGP
A multi-purpose extensible self-adaptive evolutionary algorithm
MicroGP (µGP, ugp) is a versatile optimizer able to outperform both human experts and conventional heuristics in finding the optimal solution of hard problems. It is an evolutionary algorithm since it mimics some principles of the Neo-Darwinian paradigm. ⚠️ A new version is available on https://github.com/squillero/microgp4 -
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AAARF, written in PERL and with numerous adjustable parameters, identifies sequence overlaps in small shotgun sequence datasets and walks them out to create long pseudomolecules representing the most abundant repeats in a genome.
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PRIMUS
Pedigree Reconstruction and Identification of a Maximum Unrelated Set
NEW: Download new version with Pedigree Reconstruction at primus.gs.washington.edu This versions is outdated and incomplete. Please visit the new website for the complete version of PRIMUS. We present a method adapted from graph theory that always identifies the maximum set of unrelated individuals in any dataset, and allows weighting parameters to be utilized in unrelated sample selection. PRIMUS reads in user-generated IBD estimates and outputs the maximum possible set of unrelated... -
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SimpleMap
A tool to streamline high density genetic linkage group constrcution
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SEO & SEM - Marketing Text Writer
Open Source SEO & SEM Text Creation Tools for free Article Writer
Open Source Tool for Search Engine Optimization (SEO & SEM) used for automatic content processing. These SEO Content Genrators and Article Writers based on Text... -
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HRSS
Hybrid Relative Specificity Similarity based on Gene Ontology
This software provides a hybrid GO-based semantic similarity algorithm for evaluating the functional similarity between GO terms or gene products. The software uses the pre-downloaded GO database files and the GO annotation files. It allows the users to set organisms, and evidence codes ignored. The software is composed of five modules, getGODAG, getGOAnno, hrssmatrix, hrsstps and hrsspps. -
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hrefinder
Detection of homologous recombination events from SNP data
This software detects homologous recombination events (HREs) from SNP data. Based on SNP alleles calls and locations, it breaks the genomes into locally colinear blocks, and looks for cases where SNPs do not agree with the vertical pattern of inheritance in a phylogeny. It applies a dynamic programming algorithm to model whether changes within a block are likely a result of mutations, sequencing errors, or HRE. -
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HPeak
A HMM-based algorithm for defining enriched regions from ChIP-seq data
HPeak is a hidden Markov model-based approach that can accurately pinpoint regions to where significantly more sequence reads map. Testing on real data shows that these regions are indeed highly enriched by the right protein binding sites. Command (single-end): perl /compbio/software/HPeak3/HPeak.pl -sp HUMAN/MOUSE -format BED -t TREATMENT.inp -c CONTROL.inp -n OUTPUTPREFIX -fmin 100 -fmax 300 -r 36 -ann -wig -seq -interfiles Command (pair-end): perl /compbio/software/HPeak3/HPeak.pl... -
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Simple Fast Dictionary
Simple, small and fast dictionary lib on C
The library does quick search of dictionary words in arbitrary input strings. Known problems are known. :) See appropriate section in documentation. Also, only ASCII words and strings for now. -
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SimBac is a software package for simulating bacterial genome evolution. It outputs samples of DNA sequences at each generation & allows testing of major evolutionary mechanisms, including mutation, recombination, genetic drift, and natural selection.
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The Generic Genetic Studies Database (GGSD) is a web-based, relational database driven data management software package for the management of large scale genetic studies.
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breve is a free, open-source 3D multi-agent simulation package designed for simulating decentralized systems and artificial life.
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VCAKE is a genetic sequence assembler capable of assembling millions of small nucleotide reads even in the presence of sequencing error. This software is currently geared towards de novo assembly of Illumina's Solexa Sequencing data.
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pythag is an algorithm and script for computing primitive Pythagorean triples using the command line. Has an option to output to a file. It also has an option to output to a graph using GLUT, to which it now depends.
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N-stage worm propagated via SSH. It executes commands in a given list of hosts and copies files to them with rsync. The paths for its propagation to the cluster are configurable. It offers a scalable/reliable transport API thanks to its adaptive algorithm
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NAC is a collection of tools for cryptography. The goal is to provide simple-to-use crypto tools (like an OTP, String and number generator, public key algorithm...) you can use under Linux, Windows...
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A collection of implementations of the Lovins stemmer as described in "Development of a Stemming Algorithm" by Julie Beth Lovins (published in "Mechanical translation and computational linguistics", 11:22-31, 1968).
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The goal of the Rats and Mazes project is to build a simple genetic algorithm to find general solutions to random non-cyclic single path mazes. I believe that the solutions will tend towards either the right/left-hand rule.
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The SP is a tool is a tool to research for automatic synthesis of protocols using genetic programming. This tool will allow the construction of heuristics to apply techniques simulation and validation of models.
