Search Results for "global alignment"
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Showing 16 open source projects for "global alignment"
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openTSNE
Extensible, parallel implementations of t-SNE
openTSNE is a modular Python implementation of t-Distributed Stochasitc Neighbor Embedding (t-SNE) [1], a popular dimensionality-reduction algorithm for visualizing high-dimensional data sets. openTSNE incorporates the latest improvements to the t-SNE algorithm, including the ability to add new data points to existing embeddings [2], massive speed improvements [3] [4] [5], enabling t-SNE to scale to millions of data points, and various tricks to improve the global alignment of the resulting visualizations. -
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GLM-4.6
Agentic, Reasoning, and Coding (ARC) foundation models
GLM-4.6 is the latest iteration of Zhipu AI’s foundation model, delivering significant advancements over GLM-4.5. It introduces an extended 200K token context window, enabling more sophisticated long-context reasoning and agentic workflows. The model achieves superior coding performance, excelling in benchmarks and practical coding assistants such as Claude Code, Cline, Roo Code, and Kilo Code. Its reasoning capabilities have been strengthened, including improved tool usage during inference... -
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HunyuanWorld-Voyager
RGBD video generation model conditioned on camera input
HunyuanWorld-Voyager is a next-generation video diffusion framework developed by Tencent-Hunyuan for generating world-consistent 3D scene videos from a single input image. By leveraging user-defined camera paths, it enables immersive scene exploration and supports controllable video synthesis with high realism. The system jointly produces aligned RGB and depth video sequences, making it directly applicable to 3D reconstruction tasks. At its core, Voyager integrates a world-consistent video... -
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MeRead
A RSS reader built with Flutter and designed with Material You
A concise and easy-to-use RSS reader built with Flutter and designed with Material You. -
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CView
Alignment viewer that incorporates a dynamic graphical network.
> CView wiki: https://sourceforge.net/p/cview/wiki/Home/ Related Software: 1. CStone: https://sourceforge.net/projects/cstone/ 2. CSReadGen: https://sourceforge.net/projects/csreadgen/ 3. CView: (See wiki) 4. ChimSim: https://sourceforge.net/projects/chimsim/ 5. TVScript: https://sourceforge.net/projects/tvscript/ 6. SeQuester: https://sourceforge.net/projects/sequester/ 7. TreeScope: https://sourceforge.net/projects/treescope/ -
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Covidex
Ultra fast and accurate subtyping tool of viral genomes.
Viral subtypes or clades represent clusters among isolates from the global population of a defined species. Subtypification is relevant for studies on virus epidemiology, evolution and pathogenesis. In this sense, Covidex was developed as an open source alignment-free machine learning subtyping tool. It is a shiny app that allows fast and accurate classification of viral genomes in pre-defined clusters. -
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XIVO
X Inertial-aided Visual Odometry
...It performs auto-calibration of the relative pose between the camera and the IMU as well as the time-stamp alignment. -
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Zika-RNAseq-Pipeline
An open RNA-Seq data analysis pipeline tutorial
RNA-seq analysis is becoming a standard method for global gene expression profiling. However, open and standard pipelines to perform RNA-seq analysis by non-experts remain challenging due to the large size of the raw data files and the hardware requirements for running the alignment step. Here we introduce a reproducible open source RNA-seq pipeline delivered as an IPython notebook and a Docker image. -
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pPGallery
Free Joomla! plugin to create a simple image gallery.
** minor bug fix to work with J! 3.6.x, current version: 4.316x ** /03.Aug.16 Free Joomla! content-plugin to create a simple image gallery based on 'prettyPhoto' display engine (a jQuery lightbox clone: http://www.no-margin-for-errors.com/projects/prettyPhoto-jquery-lightbox-clone). Images from folders or directly inserted into the content/article can be processed with automatic thumbnail generation. For tutorials and more detailed information refer to the Wiki: ... -
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ncmock
NetCDF mock data generator.
...Variables can be any type and filled with data in 5 ways, either a constant, a checker pattern, randoms, linear range, or a sombrero ripple function, all of which can be animated too if they use a record dimension. Global and variable attributes can also be created. Esoteric controls exist for choosing alignment, blocksize, file flavor (classic or HDF5), prefill, initial size, and header pad. ncmock has throughput and peak memory calipers, so it can also be used as a benchmark tool -
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...It uses a dynamic programming algorithm to align each query DNA sequence against a set of target protein sequences, produces frameshift-corrected protein and DNA sequences and an optimal global or local protein alignment. It also helps filter out non-target reads. The online version of FrameBot is available on http://fungene.cme.msu.edu/FunGenePipeline, tutorial http://rdp.cme.msu.edu/tutorials/framebot/RDPtutorial_FRAMEBOT.html. Updates: FrameBot now uses a kmer pre-filtering heuristic for no-metric-search. This pre-filtering may increase the speed by one to two orders of magnitude. ...
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NeedlemanWunsch
Fast global sequence alignment for the masses!
MOVED TO GITHUB: https://github.com/noporpoise/seq-align Global optimal sequence alignment using the Needleman-Wunsch algorithm. Aligns DNA, RNA, protein sequence and more! See our sister project local alignment using Smith-Waterman: http://sourceforge.net/projects/smithwaterman/ -
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SmithWaterman
Fast local sequence alignment for the masses!
MOVED TO GITHUB: https://github.com/noporpoise/seq-align An implementation of the Smith-Waterman local sequence alignment algorithm. See our sister project global alignment using Needleman-Wunsch: http://sourceforge.net/projects/needlemanwunsch/ -
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C++ library for protein sequence profile to profile alignment. Implementing numerous known alignment variants in a flexible and manageable architecture.
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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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