Search Results for "algorithm" - Page 5
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Showing 144 open source projects for "algorithm"
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Algorithm Based Automatic Contiguation of Assembled sequences (ABACAS) is an integrated platform for quickly contiguating reference based assemblies.
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BiVeS - Biochemical Model Versioning System BiVeS is a tool based on the XMLDiff algorithm. You can think of it as a kind of SVN for models with biological or chemical background encoded in XML.
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Text2Genome is a set of scripts to extract nucleotide sequences from scientific articles and to map them to genomes and genes using a local alignment algorithm (BLAST/BLAT)
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This library is a lightweight implementation of genetic algorithm, contains the most popular types of chromosomes and the basic algorithms for selection, elitism, crossing and mutation.
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CNV Workshop is a web-enabled platform for analyzing genome variation such as copy number variation (CNV). Learn about CNV Workshop in our associated BMC Bioinformatics manuscript: http://www.biomedcentral.com/1471-2105/11/74
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BorderFlow implements a general-purpose graph clustering algorithm. It maximizes the inner to outer flow ratio from the border of each cluster to the rest of the graph.
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Juggernaut is a high throughput out of core sequence assembly algorithm. This program is very useful in assembly projects involving massive number of short reads which originate from high coverage of the genome.
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CheMecher is a fully-featured chemical simulator that supports an arbitrary number of reaction steps and chemical species. Uses the Runge-Kutta algorithm for numeric solutions.
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Multi-functional batch sequence aligner incorporating Needleman-Wunsch, Smith-Waterman and Oommen-Kashyap algorithms along with compound alignment of secondary sequences.
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CEGA is a highly extendable layout plugin for Cytoscape based on an Evolutionary Algorithm. In contrast to other layout algorithms, CEGA lets users decide which features are important for the visualization of their graphs.
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D-finder is a bioinformatic search algorithm for the identification of D-sites in JNK interacting proteins. The algorithm is a combination of pattern matching and a hidden markov model (HMM) based on a training set of known JNK D-sites.
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This is an global sequence alignment tool (GSA) created using visual basic 6.0. In this software, Needleman & Wunsch algorithm is used.
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TaxonFinder is an application that annotates taxon found in literature. The application harnesses a hybrid algorithm that is necessarily a combination of morphological analysis, dictionary lookup and Levenstein Distance algorithm.
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An efficient implementation of the Smith-Waterman algorithm that takes advantage of SIMD instruction sets in modern CPUs. The Smith-Waterman algorithm is used for sequence alignment in bioinformatics.
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This is a reference implementation of snoBAC, a Bayesian Classifier designed to predict box H/ACA snoRNAs in Caenorhabditis nematode genomes. For details of algorithm and data, see Wang and Ruvinsky (2009) RNA in press.
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This project implements an algorithm for segmenting protein sequences into smaller meaningful blocks. The method is based on the pure statistical approach and it uses an analogy between proteins and natural language.
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Shape is a molecular conformation prediction program. It uses a genetic algorithm to efficiently search the conformational space of a biomolecule and then clusters the results. It is very simple to use.
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Java GUI to analyze one (or more, in batch mode) datasets with several feature selection methods at the same time and also performing an "ensemble" analysis. It can be easily extended to include any feature selection algorithm.
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ANT is a lightweight implementation in C of a kind of artificial neural net called Multilayer Perceptron, which uses the backpropagation algorithm as learning method. The package includes an introductory example to start using artificial neural nets.
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A polynomial-time algorithm for constructing level-2 phylogenetic networks from dense sets of rooted triplets.
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The program predicts the optimal folding of all consecutive substrings of length L of an RNA sequence of length N in O(NL) time. The algorithm is based on two papers: Wexler, Zilberstein, Ziv-Ukelson (2007), and Horesh, Wexler, Ziv-Ukelson ,Unger (2008)
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Java API for implementing any kind of Genetic Algorithm and Genetic Programming applications quickly and easily. Contains a wide range of ready-to-use GA and GP algorithms and operators to be plugged-in or extended. Includes Tutorials and Examples.
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