Search Results for "algorithm" - Page 6
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Showing 523 open source projects for "algorithm"
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MSAProbs: Multiple Sequence Alignment
One of the most accurate multiple protein sequence aligners
MSAProbs is an open-source protein multiple sequence ailgnment algorithm, achieving the stastistically highest alignment accuracy on popular benchmarks: BALIBASE, PREFAB, SABMARK, OXBENCH, compared to ClustalW, MAFFT, MUSCLE, ProbCons and Probalign. -
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skewer
A fast and sensitive adapter trimmer for illumina paired-end sequences
This program implements a novel dynamic programming algorithm dedicated to the task of adapter trimming and it is specially designed for processing illumina paired-end sequences. -
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ShaSeSha
Implementations of Shamir's Secret Sharing algorithm
Javascript, Python, C++ implementations of Shamir's Secret Sharing algorithm. This is very much a work in progress, and while the functionality is there to split and join, it needs work, cleanup, documentation, profiling and testing. It is only provided in the hopes it may be useful. I make absolutely NO guarantees or warranties, not even of merchantability, either expressed or implied, and do not make any claims about the security or reliability of this project. I do not authorize it's... -
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PortOpt
A portfolio-optimizer using Markowitz(1952) mean-variance model
... portfolio. In order to minimise the variance it internally uses QuadProg++, a library that implement the algorithm of Goldfarb and Idnani for the solution of a (convex) Quadratic Programming problem by means of an active-set dual method. This solution is very efficient as it allows to solve hundred of thousand of portfolio problems in seconds. PortOpt runs as a text/console tool so it can be easily used in your own scripts. -
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PopED lite
Simple, Fast, Intuitive optimal design software for preclin PKPD study
In order to maximise model based understanding of pharmacokinetic-pharmacodynamic (PKPD) studies, it is essential to choose sensible dosages and sampling times for experiments. PopED lite can help you improve your experimental design by algorithmically searching through possible experimental designs and suggesting the optimal experimental design. The algorithm is based on mathematically sound optimal design theory; however, PopED lite is made for users without any background in optimal... -
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BONDA3D Designer
3D Contents Moding Tool
... for modifying objects such as merge, subtract, intersect, etc. - Display algorithm to observe the relations with cost, volume, area and model. If you send various proposals and bugs about BONDA3D to us, we will reflect them in the ongoing product development. Thank you for your continuous interest and encouragement. -
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LaNet-vi provides images of large scale networks on a two-dimensional layout. The algorithm is based on the k-core and k-dense (m-core) decomposition. For more details see http://lanet-vi.fi.uba.ar.
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Adaptive Difficulty Chinese Chess
A Chinese chess game including an adaptive computer opponent.
This project is an application of POSM algorithm on Chinese chess computer player. A computer player is implemented, which will adapt to the its opponent by adjusting its playing strength accordingly. -
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This software searches the potential energy surface of small to medium size atomic systems for global minima using quantum ab initio techniques. It performs bond rotations and molecule translations and rotations on a Linux cluster with MPI.
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New Terrain and 3D Map System
a very lightweight advanced terrain-rendering and 3D map rendering sys
... not released yet) 3. Seme as point 2.. Multithread terrain-rendering, roads on it, and vehicles to go around. The most important part is terrain-rendering. The Algorithm at the heart of it features my first and second theorem abut polygonal surface approximation. It took something like 2 years to develop it. It's technically a view-dependent, continuous dynamic level-of-detail rendering algorithm. Main features are simplicity and documentation. Does easily a 4k x 4k terrain, but also much more. -
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FlightCraft3D: The Return
extreme 3D flight simulator with advanced terrain rendering
A rough, 3D extreme flight simulator in which there's a large terrain on which one can land: as the terrain-rendering is advanced and thus terrain is large, detailed and well visible, one can do wild flights in valleys, one can experiment with landing in any casual point of a wild, colorful area including mountous, hilly and flatty areas as well. The flightmodel is primitive here, but acceptable. I will try to do a second release in which the JSBSim module will be used to provide a more... -
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tiny-hyphenator
C++ Library to hyphenate a text
Use this class to achieve efficient and mostly exact word hyphenations. Currently the only language supported is German, but it can very easily be adapted to support other languages. This library spans ~370 lines of C++ code. At the moment there is no real documentation, pleas refer to the comments in the code, they should be quite helpful. A sample is also included. This library is not based on any algorithm published on the internet or elsewhere and it works without a dictionary. The Library... -
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libtext_bayes
Naive Bayes algorithm text classifier C++ library...
This is a Naive Bayes text classifier library to C++, you can classify SPAM messages, genes, sentiment types in texts. Naive Bayes has been studied extensively since the 1950s. It was introduced under a different name into the text retrieval community in the early 1960s, and remains a popular (baseline) method for text categorization, the problem of judging documents as belonging to one category or the other (such as spam or legitimate, sports or politics, etc.) with word frequencies as... -
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LightSpMV
lightweight GPU-based sparse matrix-vector multiplication (SpMV)
LightSpMV is a novel CUDA-compatible sparse matrix-vector multiplication (SpMv) algorithm using the standard compressed sparse row (CSR) storage format. We have evaluated LightSpMV using various sparse matrices and further compared it to the CSR-based SpMV subprograms in the state-of-the-art CUSP and cuSPARSE. Performance evaluation reveals that on a single Tesla K40c GPU, LightSpMV is superior to both CUSP and cuSPARSE, with a speedup of up to 2.60 and 2.63 over CUSP, and up to 1.93 and 1.79... -
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qcv
Computer Vision Framework Library (for Linux)
...++ interface has more features allowing the user to run and analyze complex computer vision algorithm in a few lines of code (see the stereo and surf examples). QCV offers a 2D visualization tool, an on-line on-the-fly parameter editor, a clock tool to evaluate computation times, and a control tool to manipulate input video and sequences of images. Multiple application examples that demonstrate the main features of this framework are provided in the last release. Check it out! -
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SoftSV
Calling structural variations. The soft way.
SoftSV is a tool for the detection of small and large deletions, inversions, tandem duplications and translocations from paired-end sequencing data. It uses aberrant paired-end mappings to determine approximative breakpoint regions and refines the breakpoints by analysing soft-clipped sequences for potential split-reads. For more information about the algorithm and an evaluation, have a look at this publication: "Robust and exact structural variation detection with paired-end and soft... -
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NCrypted
NCrypted - simple file encryption software with GPU support
NCrypted is a simple file encryption software. It is implemented on top of AES 128-bit algorithm. This software was designed to be as simple as possible, so you won't find any fancy, flashy gui elements or complicated advanced options. You can also use it directly from command line. NCrypted can automatically detect and take advantage of your NVidia graphics card to speed up the file processing. -
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A toolkit in C++ and python to process both experimental and simulation data of colloidal particles. Includes among others * a multiscale particle tracking algorithm [1] whose C++ implementation is optimised for 3D confocal data. Python implementation is more versatile (2D and 3D data). * a Leica file reader, * Steindhard bond orientational order calculation * a VTK file writer 1. Leocmach, M. & Tanaka, H. A novel particle tracking method with individual particle size measurement...
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SWAPHI-LS: Alignment on Xeon Phi Cluster
Smith-Waterman long DNA sequence alignment on Xeon Phi clusters
The first parallel Smith-Waterman algorithm exploiting Intel Xeon Phi clusters to accelerate the alignment of long DNA sequences. This algorithm is written in C++ (with a set of SIMD intrinsic extensions), OpenMP and MPI. The performance evaluation revealed that our algorithm achieves very stable performance, and yields a performance of up to 30.1 GCUPS on a single Xeon Phi and up to 111.4 GCUPS on four Xeon Phis sharing a host. -
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HeaDDaCHe
Hashed dynamic determinants for convex hulls
Description: We propose and implement in C++ the hashed dynamic determinants scheme. This consists of efficient implementations of dynamic determinant algorithms and a hash table that stores intermediate results (matrices and determinants) in order to be used in subsequent steps of the algorithm. Related papers: V.Fisikopoulos, L.Peñaranda. Faster Geometric Algorithms via Dynamic Determinant Computation. In Algorithms – ESA 2012, Lecture Notes in Computer Science Volume 7501, 2012... -
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RT-alignment
Graph-based time alignment algorithms for multiple LC-MS datasets
... changes under different conditions. The main challenge in this task lies in correcting retention time shifts, which are inevitable even on the same instrument and under the same elution conditions. For large-scale studies, multiple instruments or multi-week experiments are often required, which exacerbates the problem. We present a new graph-based time alignment algorithm that can align these less similar LC-MS maps, which cannot be effectively handled by existing methods. -
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SWAPHI: Smith-Waterman on Intel Xeon Phi
The first protein sequence database search on shared-host Xeon Phis
The first parallel algorithm to accelerate the Smith-Waterman protein database search on shared-host multiple Intel Xeon Phi coprocessors. By searching against the UniProtKB/TrEMBL database, SWAPHI achieves a performance of up to 58.8 billion cell updates per second (GCUPS) on a single Xeon Phi and up to 228.4 GCUPS on four Xeon Phis. -
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CUDAlign
CUDAlign is a tool that aligns huge DNA sequences in CUDA capable GPUs
CUDAlign is a tool able to align pairwise DNA sequences of unrestricted size in CUDA GPUs, using the Smith-Waterman algorithm combined with Myers-Miller. It produces the optimal alignment of 1 million base sequences in 45 seconds using a GTX 560 Ti. Many optimizations are being developed for this software. Look at the following papers for detailed information: [1] Edans Sandes, Alba Melo. Retrieving Smith-Waterman Alignments with Optimizations for Megabase Biological Sequences using GPU. IEEE... -
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Glycosylation Microviewer
An application create, simulate and adjust N-linked glycosylation.
Glycosylation Microviewer is an application that create N-linked glycosylation raction network. The model used in the application is based on two significant papers: 1.1997 Pablo Umana, James E.Bailey A Mathematical Model of N-linked Glycoform Biosynthesis. 2.2005 Frederick J.Krambeck, Michael J.Betenbaugh A Mathematical Model of N-linked Glycosylation. The application allow to simulate the network in dynamic form with various ODE solvers(Euler, Runge-Kutta etc). Genetic Algorithm... -
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SplitMEM
Graphical pan-genome analysis with suffix skips
With the rise of improved sequencing technologies, genomics is expanding from a single reference per species paradigm into a more comprehensive pan-genome approach with multiple individuals represented and analyzed together. Here we introduce a novel O(n log n) time and space algorithm called splitMEM, that directly constructs the compressed de Bruijn graph for a pan-genome of total length n. To achieve this time complexity, we augment the suffix tree with suffix skips, a new construct...
