needleman-wunsch

There are 81 repositories under needleman-wunsch topic.

  • kensho-technologies/sequence_align

    Efficient implementations of Needleman-Wunsch and other sequence alignment algorithms written in Rust with Python bindings via PyO3.

    Language:Python71484

  • jonblack/cmpgpx

    Show the differences between GPX files

    Language:Python635421

  • CMU-SAFARI/SneakySnake

    SneakySnake:snake: is the first and the only pre-alignment filtering algorithm that works efficiently and fast on modern CPU, FPGA, and GPU architectures. It greatly (by more than two orders of magnitude) expedites sequence alignment calculation for both short and long reads. Described in the Bioinformatics (2020) by Alser et al. https://arxiv.org/abs/1910.09020.

    Language:VHDL519311

  • scastlara/minineedle

    Needleman-Wunsch and Smith-Waterman algorithms in python

    Language:Python47147

  • drdrsh/Needleman-Wunsch

    Interactive Visualization of Needleman-Wunsch Algorithm in Javascript

    Language:JavaScript424417

  • lorenzocestaro/seqalign

    Collection of sequence alignment algorithms.

    Language:JavaScript26213

  • lukereichold/SpeechTimestamper

    Generate an accurate, timestamped transcript given an audio file and its text using Google Cloud's Speech-to-Text API via gRPC.

    Language:Swift21221

  • mmtechslv/nwunch

    Implementation of Needleman-Wunsch algorithm in Python Using Nested Functions.

    Language:Python13005

  • robertaboukhalil/alignment-sandbox

    Tool for exploring sequence alignment algorithms

    Language:Svelte13110

  • aziele/pairwise-sequence-alignment

    A Python module to calculate alignment between two sequences using EMBOSS' needle, stretcher, and water

    Language:Python12203

  • masyagin1998/bio-alignment

    Implementation of Needleman-Wunsch, Smith-Waterman, Hirschberg and affine bioinformatics algorithms for alighning biological sequences

    Language:C12200

  • althonos/pyopal

    Cython bindings and Python interface to Opal, a SIMD-accelerated database search aligner.

    Language:Cython9361

  • bharath3794/Algorithms-Illuminated---Part-3

    This is the implementation of 3rd Part in 3-Part Series of Algorithms Illuminated Book. All Implementations in this repository are written in both Python and Golang. Single IPython Notebook contains all Algorithms given in this Part 3.

    Language:Jupyter Notebook9207

  • oboes/gotoh

    Short implementation (~500 lines) of the Gotoh algorithm, a.k.a. Needleman-Wunsch with affine gap penalties.

    Language:C9106

  • CMU-SAFARI/Molecules2Variations

    The first work to provide a comprehensive survey of a prominent set of algorithmic improvement and hardware acceleration efforts for the entire genome analysis pipeline used for the three most prominent sequencing data, short reads (Illumina), ultra-long reads (ONT), and accurate long reads (HiFi). Described in arXiv (2022) by Alser et al. https://arxiv.org/abs/2205.07957

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  • affine-gaps

    gata-bio/affine-gaps

    Less-wrong single-file Numba-accelerated Python implementation of Gotoh affine gap penalty extensions for the Needleman–Wunsch, Smith-Waterman, and Levenshtein algorithms for sequence alignment

    Language:Python8120

  • DulanDias/DNA-Sequence-Alignment

    DNA Sequence Alignment with Dynamic Programming Implementation using the Needleman-Wunsch Algorithm and Smith-Waterman Algorithm.

    Language:Java7112

  • Mangul-Lab-USC/review-technology-dictates-algorithms

    A systematic survey of algorithmic foundations and methodologies across 107 alignment methods (1988-2021), for both short and long reads. We provide a rigorous experimental evaluation of 11 read aligners to demonstrate the effect of these underlying algorithms on speed and efficiency of read alignment. Described by Alser et al. at https://arxiv.org/abs/2003.00110.

    Language:Jupyter Notebook7303

  • abdullahmujahidali/Bio-Infomatics

    Use the Needleman-Wunsch algorithm to align two sequences: s1 and s2. Assume that a match = +2, mismatch = -2, gap = -2

    Language:Python620

  • Pawan300/Bioinformatics

    Language:Python6100

  • psykhi/sequencing

    Sequence alignment algorithms

    Language:Go6100

  • zumrudu-anka/cpp-openmp-needleman-wunsch

    :microscope: :checkered_flag: Comparison of DNA Sequences

    Language:C++6002

  • benhid/NeedlemanWunschPy

    This code is meant for educational purposes only! Sequence alignment in Python 3.x using Needleman–Wunsch algorithm. Reference code from TyMA (2017 - University of Málaga)

    Language:Python5102

  • joergen7/lib_dp

    Dynamic Programming in Erlang.

    Language:Erlang5301

  • SleekPanther/sequence-alignment

    Sequence Alignment (Needleman–Wunsch Algorithm using Dynamic Programming) for aligning sequences (words, sentences, DNA etc.)

    Language:Java5103

  • hanaecarrie/genetics-multiple-alignment

    star alignment method implementation for multiple DNA sequences alignment

    Language:Jupyter Notebook4102

  • mstfymrtc/NeedlemanWunsch

    C# implementation of Needleman-Wunsch global sequence alignment algorithm.

    Language:C#4111

  • b-ashford/cacoepy

    Tools related to mispronunciation diagnosis detection (MDD) systems.

    Language:Python3100

  • d-dawg78/COMP561-Final-Project

    McGill University - Computational Biology Methods and Research Project

    Language:Python3200

  • Enescigdem/SequenceAlignment

    Global and Local Sequence Alignment

    Language:Python3100

  • FrancisLawlor/NeedlemanWunsch

    An implementation of the Needleman-Wunsch algorithm for finding the best global alignment of two nucleotides.

    Language:Java3203

  • huutuongtu/MDD-Metric

    This is Mispronunciation detection and diagnosis Score Metric

    Language:Python3101

  • lozaeric/pymsearch

    Este es un simple buscador que permite encontrar palabras clave similares a una palabra buscada. Para realizar esto, verifica los caracteres que coinciden entre ambas utilizando el algoritmo Needleman-Wunsch.

    Language:PHP3101

  • pityka/pairwisealignment

    pairwise sequence alignment in scala

    Language:Scala3201

  • zenodeapp/pairwise-alignments

    Solidity implementations of well-known pairwise alignment methods such as Needleman-Wunsch's global sequence alignment and the Smith-Waterman local sequence alignment algorithm.

    Language:Solidity3142

  • hernanmd/class-diff

    A Pharo classes comparer

    Language:Smalltalk234