needleman-wunsch

There are 0 repository 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.
hirschberg needleman-wunsch pyo3 python rust sequence-alignment bioinformatics natural-language-processing nlp
Language:Python 63
jonblack / cmpgpx
Show the differences between GPX files
alignment gpx needleman-wunsch
Language:Python 61
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.
sequence-aligner fpga gpu hardware-accelerator minimap2 edlib smith-waterman needleman-wunsch pre-alignment-filtering sequence-alignment long-reads short-reads wavefront-alignment
Language:VHDL 47
scastlara / minineedle
Needleman-Wunsch and Smith-Waterman algorithms in python
alignment algorithm needleman-wunsch smith-waterman
Language:Python 44
drdrsh / Needleman-Wunsch
Interactive Visualization of Needleman-Wunsch Algorithm in Javascript
alignment javascript needleman-wunsch
Language:JavaScript 42
lorenzocestaro / seqalign
Collection of sequence alignment algorithms.
sequence-alignment smith-waterman needleman-wunsch string-alignment string-distance hacktoberfest
Language:JavaScript 25
lukereichold / SpeechTimestamper
Generate an accurate, timestamped transcript given an audio file and its text using Google Cloud's Speech-to-Text API via gRPC.
natural-language-processing nlp audio-transcribing speech-to-text timestamp grpc gcp string-alignment needleman-wunsch google-cloud-platform karaoke protobuf transcription gcp-speech karaoke-maker
Language:Swift 19
mmtechslv / nwunch
Implementation of Needleman-Wunsch algorithm in Python Using Nested Functions.
needleman-wunsch needleman-wunsch-algorithm bioinformatics alignment sequence-alignment alignment-algorithm python demo
Language:Python 13
masyagin1998 / bio-alignment
Implementation of Needleman-Wunsch, Smith-Waterman, Hirschberg and affine bioinformatics algorithms for alighning biological sequences
needleman-wunsch comparing-biological-sequences bioinformatics dynamic-programming hirschberg smith-waterman
Language:C 12
oboes / gotoh
Short implementation (~500 lines) of the Gotoh algorithm, a.k.a. Needleman-Wunsch with affine gap penalties.
needleman-wunsch alignment bioinformatics dynamic-programming
Language:C 9
althonos / pyopal
Cython bindings and Python interface to Opal, a SIMD-accelerated database search aligner.
bioinformatics cython-library cython-wrapper genomics needleman-wunsch python-bindings python-library sequence-alignment simd smith-waterman
Language:Python 8
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.
algorithms-illuminated bellman-ford-algorithm coursera-algorithms-specialization disjoint-set dynamic-programming floyd-warshall-algorithm golang greedy-algorithms huffman-algorithm knapsack-problem kruskal-algorithm needleman-wunsch optimal-binary-search-tree prim-algorithm prims-algorithm python union-find weighted-independent-set
Language:Jupyter Notebook 8
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
basecalling bioinformatics fast5 fasta fastq genome-analysis hifi illumina minimap2 needleman-wunsch quality-control read-mapping sam sequence-alignment sequencing smith-waterman variant-calling vcf wavefront-alignment wfa
8
abdullahmujahidali / Bio-Infomatics
Use the Needleman-Wunsch algorithm to align two sequences: s1 and s2. Assume that a match = +2, mismatch = -2, gap = -2
python3 python bioinformatics needleman-wunsch needleman
Language:Python 6
affine-gaps
ashvardanian / 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
bioinformatics protein protein-sequences sequence-alignment jit levenshtein-algorithm levenshtein-distance needleman-wunsch search smith-waterman string-search
Language:Python 6
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.
read-alignments needleman-wunsch smith-waterman heuristics read-mapping sequence-alignment hts nanopore-sequencing illumina-sequencing pacbio-sequencing hifi-read genome-analysis
Language:Jupyter Notebook 6
Pawan300 / Bioinformatics
bioinformatics needleman-wunsch smithwater dotplot slidingwindow
Language:Python 6
psykhi / sequencing
Sequence alignment algorithms
bioinformatics needleman-wunsch sequence-alignment levenshtein-distance golang go
Language:Go 6
zumrudu-anka / cpp-openmp-needleman-wunsch
:microscope: :checkered_flag: Comparison of DNA Sequences
needleman-wunsch-algorithm needleman-wunsch needlemanwunsch openmp cpp
Language:C++ 6
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)
bioinformatics sequence-alignments needleman-wunsch
Language:Python 5
DulanDias / DNA-Sequence-Alignment
DNA Sequence Alignment with Dynamic Programming Implementation using the Needleman-Wunsch Algorithm and Smith-Waterman Algorithm.
java sequence-alignment dna-sequences dna computational-biology bioinformatics dynamic-programming needleman-wunsch needleman-wunsch-algorithm smith-waterman smithsmith-waterman-algorithm
Language:Java 5
joergen7 / lib_dp
Dynamic Programming in Erlang.
alignment erlang needleman-wunsch similarity-score smith-waterman
Language:Erlang 5
SleekPanther / sequence-alignment
Sequence Alignment (Needleman–Wunsch Algorithm using Dynamic Programming) for aligning sequences (words, sentences, DNA etc.)
dynamic-programming dynamic pseudocode optimal-substructure optimal optimality needleman-wunsch needlemanwunsch needleman wunsch algorithm algorithms algorithm-design memoization memo memorization noah-patullo noah patullo patulo
Language:Java 5
mstfymrtc / NeedlemanWunsch
C# implementation of Needleman-Wunsch global sequence alignment algorithm.
sequence-alignment needleman-wunsch dynamic-programming global-alignment
Language:C# 4
Enescigdem / SequenceAlignment
Global and Local Sequence Alignment
needleman-wunsch needleman-wunsch-algorithm smith-waterman smith-waterman-alignment global-alignment local-alignment bioinformatics
Language:Python 3
FrancisLawlor / NeedlemanWunsch
An implementation of the Needleman-Wunsch algorithm for finding the best global alignment of two nucleotides.
bioinformatics dynamic-programming needleman-wunsch
Language:Java 3
hanaecarrie / genetics-multiple-alignment
star alignment method implementation for multiple DNA sequences alignment
genetics alignment needleman-wunsch dna-sequences
Language:Jupyter Notebook 3
huutuongtu / MDD-Metric
This is Mispronunciation detection and diagnosis Score Metric
dynamic-programming mdd needleman-wunsch mdd-metric mispronunciation-detection mispronunciation-detection-metric
Language:Python 3
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.
search-engine search-algorithm php5 needleman-wunsch searching
Language:PHP 3
pityka / pairwisealignment
pairwise sequence alignment in scala
needleman-wunsch smith-waterman-gotoh wavefront-alignment scala
Language:Scala 3
robertaboukhalil / alignment-sandbox
Tool for exploring sequence alignment algorithms
bioinformatics genomics alignment algorithms smith-waterman needleman-wunsch webassembly
Language:Svelte 3
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.
algorithm alignment amino-acids dna needleman-wunsch nucleotides proteins smith-waterman substitution-matrices contracts solidity
Language:Solidity 3
danielfamiyeh / biothon
Biosequence analysis library
biosequences phylogenetic-dendrograms hierarchical-cluster-analysis bioinformatics clustalw clustering fasta gc-content hirschberg multiple-sequence-alignment needleman-wunsch pairwise-alignment sequence-alignment smith-waterman transcription
Language:Python 2
Howeng98 / Smith_Waterman_parallel
Implement parallel Smith Waterman algorithm on CUDA
smith-waterman-alignment smith-waterman-algorithm smith-waterman needleman-wunsch needleman-wunsch-algorithm cuda-programming cuda parallel-programming
Language:Cuda 2
mamutalib / Bio-informatics
Bio informatics course materials for NEUB students.
edit-distance-algorithm needleman-wunsch-algorithm neub smith-waterman-algorithm dna-transcription pdp partial-digest-problem bio-informatics bioinformatics bioinformatics-algorithms algorithm edit-distance edit-distance-algorithm-implementation edit-distance-algorithms needleman-wunsch needleman-wunsch-alignment needleman-algorithm
Language:C++ 2
sirineFoudili / DNA-comparison-and-alignment-
web application for DNA comparison, alignment and phylogenetic tree. Released on 2020.
dna adn alignement alignment alignment-free indexation bloom-filter k-mers hashing phylogenetic-tree phylogenie dna-alignment needleman-wunsch flask python bioinformatics bioinformatique
Language:JavaScript 2

needleman-wunsch

kensho-technologies / sequence_align

jonblack / cmpgpx

CMU-SAFARI / SneakySnake

scastlara / minineedle

drdrsh / Needleman-Wunsch

lorenzocestaro / seqalign

lukereichold / SpeechTimestamper

mmtechslv / nwunch

masyagin1998 / bio-alignment

oboes / gotoh

althonos / pyopal

bharath3794 / Algorithms-Illuminated---Part-3

CMU-SAFARI / Molecules2Variations

abdullahmujahidali / Bio-Infomatics

ashvardanian / affine-gaps

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

Pawan300 / Bioinformatics

psykhi / sequencing

zumrudu-anka / cpp-openmp-needleman-wunsch

benhid / NeedlemanWunschPy

DulanDias / DNA-Sequence-Alignment

joergen7 / lib_dp

SleekPanther / sequence-alignment

mstfymrtc / NeedlemanWunsch

Enescigdem / SequenceAlignment

FrancisLawlor / NeedlemanWunsch

hanaecarrie / genetics-multiple-alignment

huutuongtu / MDD-Metric

lozaeric / pymsearch

pityka / pairwisealignment

robertaboukhalil / alignment-sandbox

zenodeapp / pairwise-alignments

danielfamiyeh / biothon

Howeng98 / Smith_Waterman_parallel

mamutalib / Bio-informatics

sirineFoudili / DNA-comparison-and-alignment-