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pairwise-alignment

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pairwise-alignment /pa-bench

Benchmarking pairwise aligners

benchmark pairwise-alignment

UpdatedFeb 8, 2025
Jupyter Notebook

quim0 /WFA-GPU

GPU implementation of the Wavefront Alignment Algorithm for global, gap-affine, pairwise sequence alginment

bioinformatics gpu cuda sequence-alignment pairwise-alignment

UpdatedApr 30, 2025
C

RagnarGrootKoerkamp /sassy

Fast approximate string searching

edit-distance simd approximate-string-matching pairwise-alignment

UpdatedJun 30, 2025
Rust

aziele /pairwise-sequence-alignment

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

smith-waterman needleman-wunsch needle water global-alignment sequence-alignment emboss protein-sequence pairwise-alignment local-alignment nucleotide-sequence

UpdatedFeb 27, 2025
Python

iosonofabio /seqanpy

Fast pairwise sequence alignment using SeqAn, in Python.

python python-wrapper swig seqan sequence-alignment pairwise-alignment

UpdatedMar 23, 2019
C++

orangeSi /bam2msa

convert alignment bam to pairwise alignment or multiple sequence alignment (msa) at genome specific region

bioinformatics alignment bam msa pairwise-alignment crystal-lang

UpdatedMay 21, 2024
Crystal

nf-core /pairgenomealign

Pairwise genome comparison pipeline using the LAST software to align a list of query genomes to a target genome, and plot the results

bioinformatics genomics nextflow comparative-genomics synteny last pairwise-alignment whole-genome-alignment nf-core dot-plot

UpdatedJun 23, 2025
Nextflow

pairwise-alignment /pa-types

Basic types and functions for pairwise alignment.

library bioinformatics pairwise-alignment

UpdatedMar 22, 2024
Rust

odoluca /Fast-NW-and-SW-Pairwise-alignment-using-numba-JIT

This project includes Needleman-Wunsch and Smith-Waterman algorithms and their afine gap variations (Gotoh) written to work with Cython, PyPy and Numba. Numba JIT shows greater performance. For Best performance use gotoh_jit.py to get only the best score and use gotoh_jit_traceback to get the best alignment

python cython smith-waterman needleman-wunsch python-3-6 alignment protein-sequences numba dna-sequences pairwise pairwise-alignment pypy3 gotoh

UpdatedSep 22, 2021
Python

danielfamiyeh /biothon

Bioinformatics library

bioinformatics clustering smith-waterman needleman-wunsch fasta transcription sequence-alignment pairwise-alignment gc-content multiple-sequence-alignment clustalw hirschberg biosequences phylogenetic-dendrograms hierarchical-cluster-analysis

UpdatedJul 20, 2022
Python

danielezeobinna /Genomic-Sequence-Comparison-Code-GSCC-

This repository houses the Genomic Sequence Comparison Code (GSCC), a collection of Python scripts designed for genomic sequence analysis. Whether you're comparing suspected sequences with known reference sequences or delving into bioinformatics, GSCC provides versatile tools for pairwise alignment. Feel free to explore!

bioinformatics computational-biology python3 biopython rna-sequencing dna-sequences sequence-alignment bioinformatics-scripts genomic-data-analysis pairwise-alignment bioinformatics-tool genomics-analysis

UpdatedMar 19, 2024
Python

Ensembl /sam-alignment-reconstructor

SAM Alignment Reconstructor

bioinformatics pairwise-alignment sam-format

UpdatedJul 26, 2018
Python

pairwise-alignment /pa-generate

Generate random sequence pairs to test pairwise aligners

data-generator pairwise-alignment

UpdatedMar 20, 2025
Rust

Amirreza-Mousavi /Protein_Normalized_SW_Similarity_Score

An R script that calculates a similarity matrix for a list of protein sequences with the aid of Bleakley-Yamanishi Normalized Smith-Waterman Similarity Score.

r psa computational-biology smith-waterman protein drug-discovery protein-sequences fasta sequence similarity-score sequence-alignment similarity-matrix dti fasta-sequences pairwise-alignment local-alignment smith-waterman-alignment computer-aided-drug-design biostrings dti-prediction

UpdatedDec 23, 2021
R

nhays89 /ABC

Top Coder Problem

sequencing string-manipulation pairwise-alignment

UpdatedJan 12, 2019
Java

gpmerola /SimplePairwiseAlignment

This repository contains a simple implementation of a pairwise alignment algorithm for FASTA files using the Needleman-Wunsch algorithm.

genetics alignment pairwise-alignment

UpdatedJun 20, 2024
C++

marco-ruiz /pairwise-sequence-aligner

Applications that compute pairwise alignments of two biological sequences

bioinformatics spring-boot swing dynamic-programming sequence-alignment pairwise-alignment smith-waterman-alignment

UpdatedJun 24, 2025
Java

Zeelot1 /Geneexplorer

A bioinformatics-driven assessment of Genetically Modified Organism (GMO) status in maize and soyabeans

bioinformatics-pipeline blastn pairwise-alignment

UpdatedJun 18, 2025
Python

Abrar2652 /oist-comparative-genomics

python bioinformatics r biopython shell-script comparative-genomics sorting-algorithms-implemented bash-script searching-algorithms genome-analysis ucsc-browser pairwise-alignment matching-algorithm matplotlib-pyplot

UpdatedJan 28, 2025
Python

BCCDC-PHL /align-compare

Pipeline to make pairwise comparisons of matched fasta sequences.

bioinformatics-pipeline microbial-genomics pairwise-alignment

UpdatedNov 28, 2022
Python

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