GitHub topics: sequence-alignment
biopython/biopython
Official git repository for Biopython (originally converted from CVS)
Language: Python - Size: 71 MB - Last synced at: about 3 hours ago - Pushed at: 2 days ago - Stars: 4,611 - Forks: 1,795
bbuchfink/diamond
Accelerated BLAST compatible local sequence aligner.
Language: C++ - Size: 31.7 MB - Last synced at: 1 day ago - Pushed at: 1 day ago - Stars: 1,149 - Forks: 181
cogent3/cogent3
Comparative Genomics Toolkit 3
Language: Python - Size: 45.2 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 130 - Forks: 65
Martinsos/edlib
Lightweight, super fast C/C++ (& Python) library for sequence alignment using edit (Levenshtein) distance.
Language: C++ - Size: 4.67 MB - Last synced at: 4 days ago - Pushed at: 20 days ago - Stars: 544 - Forks: 169
torognes/vsearch
Versatile open-source tool for microbiome analysis
Language: C++ - Size: 6.71 MB - Last synced at: 3 days ago - Pushed at: 28 days ago - Stars: 700 - Forks: 127
lh3/minimap2
A versatile pairwise aligner for genomic and spliced nucleotide sequences
Language: C - Size: 1.55 MB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 1,968 - Forks: 434
algbio/emerald
EMERALD calculates safety-windows by exploring the suboptimal alignment space
Language: C++ - Size: 1.45 MB - Last synced at: 2 days ago - Pushed at: 2 days ago - Stars: 17 - Forks: 0
bibymaths/SequenceAligner
A high-performance tool for global and local sequence alignment using Needleman-Wunsch, Smith-Waterman, and LCS algorithms, accelerated with MPI, OpenMP, and SIMD for DNA and protein sequences
Language: C++ - Size: 3.15 MB - Last synced at: 7 days ago - Pushed at: 7 days ago - Stars: 0 - Forks: 0
tmaklin/kbo
Local alignment search with k-bounded matching statistics.
Language: Rust - Size: 428 KB - Last synced at: 7 days ago - Pushed at: 8 days ago - Stars: 5 - Forks: 1
jguhlin/minimap2-rs
Rust bindings to minimap2 library
Language: Jupyter Notebook - Size: 23.1 MB - Last synced at: 4 days ago - Pushed at: about 1 month ago - Stars: 99 - Forks: 17
lh3/miniprot
Align proteins to genomes with splicing and frameshift
Language: C - Size: 455 KB - Last synced at: 10 days ago - Pushed at: 10 days ago - Stars: 365 - Forks: 19
laurentnoe/iedera
subset and spaced seed design tool
Language: C++ - Size: 1.26 MB - Last synced at: 10 days ago - Pushed at: 10 days ago - Stars: 3 - Forks: 1
shenwei356/LexicMap
LexicMap: efficient sequence alignment against millions of prokaryotic genomes
Language: Go - Size: 43 MB - Last synced at: 11 days ago - Pushed at: 11 days ago - Stars: 144 - Forks: 4
moshi4/pyMSAviz
MSA(Multiple Sequence Alignment) visualization python package for sequence analysis
Language: Python - Size: 7.2 MB - Last synced at: 9 days ago - Pushed at: 6 months ago - Stars: 128 - Forks: 16
lh3/bwa
Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)
Language: C - Size: 1.7 MB - Last synced at: 11 days ago - Pushed at: 2 months ago - Stars: 1,606 - Forks: 563
RWilton/Arioc
Arioc: GPU-accelerated DNA short-read alignment
Size: 16.9 MB - Last synced at: 12 days ago - Pushed at: 12 days ago - Stars: 69 - Forks: 9
kisnikser/snack
SNACK: Sequence Normalized Alignment Comparison Kit
Language: Jupyter Notebook - Size: 601 KB - Last synced at: 12 days ago - Pushed at: 13 days ago - Stars: 1 - Forks: 0
Integrative-Transcriptomics/MUSIAL
Summarize SNV and indel information on single gene or genome level together with other relevant statistics based on .vcf files.
Language: Java - Size: 291 MB - Last synced at: 14 days ago - Pushed at: 14 days ago - Stars: 5 - Forks: 1
fullscreen-triangle/hegel
Evidence Rectification Framework for Biological Molecules
Language: JavaScript - Size: 2.11 MB - Last synced at: 15 days ago - Pushed at: 15 days ago - Stars: 1 - Forks: 0
CDCgov/MicrobeTrace Fork of AABoyles/MicrobeTrace
The Visualization Multitool for Molecular Epidemiology and Bioinformatics
Language: TypeScript - Size: 136 MB - Last synced at: 9 days ago - Pushed at: 9 days ago - Stars: 92 - Forks: 42
laurentnoe/yass
genomic alignment similarity search tool
Language: C - Size: 515 KB - Last synced at: 17 days ago - Pushed at: 17 days ago - Stars: 18 - Forks: 6
lh3/minigraph
Sequence-to-graph mapper and graph generator
Language: C - Size: 928 KB - Last synced at: 7 days ago - Pushed at: about 1 year ago - Stars: 444 - Forks: 39
nlaha/genomics-rs
Rust implementations of the Needleman-Wunsch global alignment algorithm and the Smith-Waterman local alignment algorithm
Language: Rust - Size: 659 KB - Last synced at: 19 days ago - Pushed at: 19 days ago - Stars: 0 - Forks: 0
seqan/seqan3
The modern C++ library for sequence analysis. Contains version 3 of the library and API docs.
Language: C++ - Size: 22.8 MB - Last synced at: 10 days ago - Pushed at: 20 days ago - Stars: 427 - Forks: 83
kensho-technologies/sequence_align
Efficient implementations of Needleman-Wunsch and other sequence alignment algorithms written in Rust with Python bindings via PyO3.
Language: Python - Size: 201 KB - Last synced at: 8 days ago - Pushed at: 3 months ago - Stars: 72 - Forks: 4
baku4/sigalign
A Similarity-Guided Alignment Algorithm
Language: Rust - Size: 11.7 MB - Last synced at: 23 days ago - Pushed at: 23 days ago - Stars: 26 - Forks: 4
haddocking/whiscy
Bioinformatic tool to predict structural protein-protein interfaces
Language: R - Size: 3.68 MB - Last synced at: 3 days ago - Pushed at: 11 months ago - Stars: 4 - Forks: 2
flatironinstitute/deepblast
Neural Networks for Protein Sequence Alignment
Language: Python - Size: 56.7 MB - Last synced at: 15 days ago - Pushed at: 7 months ago - Stars: 121 - Forks: 22
wurmlab/sequenceserver
Intuitive graphical web interface for running BLAST bioinformatics tool (i.e. have your own custom NCBI BLAST site!)
Language: JavaScript - Size: 124 MB - Last synced at: 10 days ago - Pushed at: 5 months ago - Stars: 282 - Forks: 113
BioJulia/BioAlignments.jl
Sequence alignment tools
Language: Julia - Size: 1.1 MB - Last synced at: 3 days ago - Pushed at: 10 months ago - Stars: 63 - Forks: 24
edouzery/BASH_Memo
A memo with more than 100 BASH commands with examples
Language: HTML - Size: 1.17 MB - Last synced at: 26 days ago - Pushed at: 26 days ago - Stars: 0 - Forks: 0
jajik123/GenAnalyzer
GenAnalyzer is a web application designed for the analysis of protein sequences, mutation detection, and exploring their links to genetic diseases. Built using Flask, this tool integrates data from UniProt and ClinVar for efficient bioinformatics analysis.
Language: JavaScript - Size: 2.03 MB - Last synced at: 30 days ago - Pushed at: 30 days ago - Stars: 0 - Forks: 0
quim0/WFA-GPU
GPU implementation of the Wavefront Alignment Algorithm for global, gap-affine, pairwise sequence alginment
Language: C - Size: 5 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 34 - Forks: 3
althonos/pymuscle5
Cython bindings and Python interface to MUSCLE v5, a highly efficient and accurate multiple sequence alignment software.
Language: Cython - Size: 115 KB - Last synced at: 3 days ago - Pushed at: about 1 year ago - Stars: 21 - Forks: 2
lignum-vitae/goombay
Python implementation of several sequence alignment algorithms such as Waterman-Smith-Beyer, Gotoh, and Needleman-Wunsch intended to calculate distance, show alignment, and display the underlying matrices.
Language: Python - Size: 217 KB - Last synced at: 19 days ago - Pushed at: about 1 month ago - Stars: 0 - Forks: 0
SamStan4/Pairwise-Sequence-Alignment-Algorithm
An implementation of the pairwise sequence alignment algorithm with an affine gap penalty implemented in C++
Language: C++ - Size: 305 KB - Last synced at: 11 days ago - Pushed at: about 1 month ago - Stars: 0 - Forks: 0
SamStan4/Genome-Scale-Comparison
Implementation of large scale genome comparisons. Utilizes McCreight Suffix tree construction algorithm as well as a modified Pairwise Sequence Alignment algorithm with an Affine Gap Penalty. Implemented in C++.
Language: C++ - Size: 66.4 KB - Last synced at: 11 days ago - Pushed at: about 1 month ago - Stars: 0 - Forks: 0
IlyinVyacheslav/BioInformatics
Gene download from NCBI database, sequence alignment and clusterization, realization of different bioinformatics algorithms within ITMO 4 sem course
Language: Jupyter Notebook - Size: 14.5 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 0 - Forks: 0
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: Python - Size: 99.6 KB - Last synced at: 8 days ago - Pushed at: about 2 months ago - Stars: 9 - Forks: 0
microsoft/bistring
Bidirectionally transformed strings
Language: Python - Size: 978 KB - Last synced at: 4 days ago - Pushed at: over 1 year ago - Stars: 368 - Forks: 17
sanderlab/alignmentviewer
Multiple sequence alignment visualizer
Language: JavaScript - Size: 9.26 MB - Last synced at: 1 day ago - Pushed at: over 2 years ago - Stars: 30 - Forks: 6
biojava/biojava
:book::microscope::coffee: BioJava is an open-source project dedicated to providing a Java library for processing biological data.
Language: Java - Size: 48.8 MB - Last synced at: about 2 months ago - Pushed at: 2 months ago - Stars: 606 - Forks: 391
MHosseinHashemi/IASBS_Bioinformatics_Course
Bioinformatics Course Material (Assignments, Final Project, etc)
Language: Jupyter Notebook - Size: 7.72 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 0 - Forks: 0
CaoTianze/plotnineseqsuite
plotnineSeqSuite: a Python package for visualizing sequence data using ggplot2 style
Language: Python - Size: 11 MB - Last synced at: 20 days ago - Pushed at: 3 months ago - Stars: 16 - Forks: 0
biocommons/uta-align
C-based Needleman-Wunsch and Smith-Waterman alignment algorithms with a Python interface.
Language: Cython - Size: 350 KB - Last synced at: about 1 month ago - Pushed at: about 1 year ago - Stars: 6 - Forks: 5
Robaina/filterSAM
Tools to filter SAM/BAM files by percent identity and percent of matched sequence
Language: Python - Size: 313 KB - Last synced at: 6 days ago - Pushed at: almost 2 years ago - Stars: 5 - Forks: 0
aziele/pairwise-sequence-alignment
A Python module to calculate alignment between two sequences using EMBOSS' needle, stretcher, and water
Language: Python - Size: 44.9 KB - Last synced at: about 1 month ago - Pushed at: 3 months ago - Stars: 13 - Forks: 3
Nonilas/Bioinformatics-2024-Projects
MATLAB Bioinformatics assignments covering sequence alignment, gene expression analysis, PCA, phylogenetics, and metabolomics.
Size: 27.5 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 1 - Forks: 0
Nazeeefa/awesome-sequencing-tech-papers
A collection of publications on comparison of high-throughput sequencing technologies.
Size: 173 KB - Last synced at: 26 days ago - Pushed at: 5 months ago - Stars: 27 - Forks: 3
tmaklin/kbo-cli
Command-line interface for the kbo local aligner.
Language: Rust - Size: 85.9 KB - Last synced at: 23 days ago - Pushed at: about 2 months ago - Stars: 0 - Forks: 1
biocommons/uta
Universal Transcript Archive: comprehensive genome-transcript alignments; multiple transcript sources, versions, and alignment methods; available as a docker image
Language: Python - Size: 14.5 MB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 63 - Forks: 25
tejarshaarigila/bioinformatics-sequence-alignment
Python implementations of the Needleman-Wunsch and Smith-Waterman sequence alignment algorithms.
Language: Python - Size: 7.81 KB - Last synced at: about 2 months ago - Pushed at: 2 months ago - Stars: 0 - Forks: 0
hallamlab/samsum
A light-weight python package for summarizing sequence coverage from SAM and BAM files
Language: Python - Size: 1.92 MB - Last synced at: 16 days ago - Pushed at: 9 months ago - Stars: 7 - Forks: 3
lh3/ksw2
Global alignment and alignment extension
Language: C - Size: 189 KB - Last synced at: 26 days ago - Pushed at: almost 2 years ago - Stars: 131 - Forks: 26
Martinsos/opal
SIMD C/C++ library for massive optimal sequence alignment (local/SW, infix, overlap, global)
Language: C++ - Size: 19 MB - Last synced at: 9 days ago - Pushed at: over 1 year ago - Stars: 38 - Forks: 10
althonos/pyfamsa
Cython bindings and Python interface to FAMSA, an algorithm for ultra-scale multiple sequence alignments.
Language: Cython - Size: 289 KB - Last synced at: 13 days ago - Pushed at: 3 months ago - Stars: 31 - Forks: 3
IbrahimTanyalcin/lexicon-mono-seq
DOM Text Based Multiple Sequence Alignment Library
Language: JavaScript - Size: 117 MB - Last synced at: about 11 hours ago - Pushed at: almost 6 years ago - Stars: 20 - Forks: 5
drostlab/orthologr
Genome wide orthology inference and dNdS estimation
Language: R - Size: 103 MB - Last synced at: about 1 month ago - Pushed at: over 1 year ago - Stars: 90 - Forks: 27
zitunstu24/CDSMatch
A Python package and command-line tool for matching IDs from two different genome annotation sources based on sequence similarity. Ideal for data reconciliation, entity resolution, and fuzzy matching tasks. 🚀
Language: Python - Size: 0 Bytes - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 0 - Forks: 0
nanxstats/ssw-r
🚀 R interface for SSW, a fast implementation of the Smith-Waterman algorithm using SIMD
Language: R - Size: 1.36 MB - Last synced at: 9 days ago - Pushed at: 9 months ago - Stars: 6 - Forks: 0
lh3/bioseq-js
For live demo, see http://lh3lh3.users.sourceforge.net/bioseq.shtml
Language: HTML - Size: 16.6 KB - Last synced at: 3 months ago - Pushed at: almost 6 years ago - Stars: 38 - Forks: 16
althonos/pyopal
Cython bindings and Python interface to Opal, a SIMD-accelerated database search aligner.
Language: Cython - Size: 281 KB - Last synced at: 3 days ago - Pushed at: 3 months ago - Stars: 9 - Forks: 1
ppillot/biomsalign
JavaScript library for Multiple Sequence Alignment
Language: TypeScript - Size: 622 KB - Last synced at: 27 days ago - Pushed at: over 1 year ago - Stars: 21 - Forks: 0
drostlab/rdiamond
Running DIAMOND2 through R
Language: R - Size: 628 KB - Last synced at: about 1 month ago - Pushed at: over 1 year ago - Stars: 7 - Forks: 2
metaphysicser/RaMA
Fast sequence alignment for centromere with RaMA
Language: C++ - Size: 152 KB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 3 - Forks: 1
benhid/pyMSA
Scoring multiple sequence alignments with Python
Language: Python - Size: 1.34 MB - Last synced at: 12 days ago - Pushed at: almost 2 years ago - Stars: 22 - Forks: 10
chchch/sanskrit-alignment
Sequence alignment and textual reconstruction for Sanskrit texts
Language: JavaScript - Size: 45.3 MB - Last synced at: about 10 hours ago - Pushed at: 4 months ago - Stars: 10 - Forks: 3
CDCgov/clean-genes
A rust crate that automatically cleans up a gene alignment by trimming to ORF and identifying and/or removing problematic sequences.
Language: Rust - Size: 186 KB - Last synced at: 9 days ago - Pushed at: 3 months ago - Stars: 1 - Forks: 2
kaua-pt/FastType
Faster you tap, Faster you win
Language: C# - Size: 539 KB - Last synced at: 3 months ago - Pushed at: 6 months ago - Stars: 2 - Forks: 0
mhahsler/rMSA
Interface to Popular Multiple Sequence Alignment Tools - R-package
Language: TeX - Size: 613 KB - Last synced at: 2 months ago - Pushed at: 9 months ago - Stars: 12 - Forks: 1
caioss/miga
MIGA is a Python package that provides a MSA (Multiple Sequence Alignment) mutual information genetic algorithm optimizer. It sorts two MSAs in a way that maximize or minimize their mutual information. The genetic algorithm solvers may run on both CPU and Nvidia GPUs.
Language: Python - Size: 295 KB - Last synced at: 16 days ago - Pushed at: over 1 year ago - Stars: 8 - Forks: 3
nbay13/toilkit
A python package for working with inputs to and outputs from the toil-rnaseq pipeline
Language: Python - Size: 784 KB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 1 - Forks: 0
GiatrasKon/sandbox.bio-Solutions
Bash scripts replicating the commands from sandbox.bio's interactive bioinformatics tutorials, organized by categories such as Data Exploration, File Formats, Quality Control, and Data Analysis.
Language: Shell - Size: 11.7 KB - Last synced at: 2 months ago - Pushed at: 4 months ago - Stars: 0 - Forks: 0
brianli314/palindrome-finder
A bioinformatics tool written in Rust to find palindromic sequences in DNA
Language: Rust - Size: 96.7 KB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 34 - Forks: 0
datasnakes/OrthoEvolution
An easy to use and comprehensive python package which aids in the analysis and visualization of orthologous genes. 🐵
Language: Python - Size: 40.6 MB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 28 - Forks: 4
nsbuitrago/parasail-rs
SIMD pairwise sequence alignment
Language: Rust - Size: 111 KB - Last synced at: about 1 month ago - Pushed at: 3 months ago - Stars: 1 - Forks: 1
TravisWheelerLab/WASITAMATchISAW
Approximate palindromes lead to overstated false match rates in benchmarks using reversed sequences
Language: Jupyter Notebook - Size: 21.8 MB - Last synced at: about 1 month ago - Pushed at: 5 months ago - Stars: 0 - Forks: 0
nsbuitrago/libparasail-sys
Rust bindings for the Parasail C library
Language: Rust - Size: 60.5 KB - Last synced at: about 16 hours ago - Pushed at: 1 day ago - Stars: 0 - Forks: 0
zhou-lab/biscuit
BISulfite-seq CUI Toolkit
Language: C - Size: 6.79 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 64 - Forks: 24
lh3/unimap
A EXPERIMENTAL fork of minimap2 optimized for assembly-to-reference alignment
Language: C - Size: 487 KB - Last synced at: 26 days ago - Pushed at: about 4 years ago - Stars: 88 - Forks: 4
johnedquinn/sequence-align
Performs DNA sequence alignment of Anopheles Gambiae (common mosquito). Speeds up execution time by a factor of ~200 by distributing computation via the HTCondor and Work Queue systems. Utilizes swaligntool to compute scores of DNA comparisons.
Language: Python - Size: 62.5 KB - Last synced at: 2 months ago - Pushed at: about 4 years ago - Stars: 0 - Forks: 0
AABoyles/MicrobeTrace
The Visualization Multitool for Molecular Epidemiology and Bioinformatics
Language: HTML - Size: 68.5 MB - Last synced at: about 2 months ago - Pushed at: 9 months ago - Stars: 12 - Forks: 42
Gagniuc/Visual-Sequence-Alignment-in-VB6
This highly visual and responsive VB6 application is an implementation of the global sequence alignment algorithm. It allows the modification of the alignment parameters (match, mismatch, gap), and it shows the pairwise alignment as well as the score matrix in real time.
Language: Visual Basic 6.0 - Size: 7.26 MB - Last synced at: 3 months ago - Pushed at: over 2 years ago - Stars: 9 - Forks: 2
HarshOza36/DNA_Sequence_Alignment
CSCI-570 Analysis Of Algorithms project at USC
Language: Python - Size: 3.08 MB - Last synced at: 3 months ago - Pushed at: about 3 years ago - Stars: 2 - Forks: 0
unikill066/BLAST-Search
Search and Alignment Tool in Bioinformatics Domain
Language: Shell - Size: 2.52 MB - Last synced at: 10 days ago - Pushed at: 6 months ago - Stars: 0 - Forks: 0
leila-kasmi-lk150/SequenceAlignment
Implementation of Sequence Alignment using Needleman-Wunsch and Smith-Waterman algorithms with fixed scoring values.
Language: Java - Size: 144 KB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 0 - Forks: 0
recalldev10/Nextflow-Genomic-Analysis-Pipeline
Bioinformatics pipeline for DNA sequence analysis implementing automated FASTQ processing and sequence alignment using Nextflow and Bowtie2. Features quality control, E. coli genome alignment, and standardized output formats for genomic research.
Language: Nextflow - Size: 0 Bytes - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 0 - Forks: 0
andrewdavidsmith/adapto-rs
Remove adaptors from short-read bisulfite sequencing data (coded in rust)
Language: Rust - Size: 72.3 KB - Last synced at: 2 months ago - Pushed at: 9 months ago - Stars: 0 - Forks: 0
hdescobarh/pairwasm_alignment
This is an experiment implementing a WebAssembly pairwise sequence alignment module in Rust 🦀.
Language: Rust - Size: 1.79 MB - Last synced at: about 10 hours ago - Pushed at: 8 months ago - Stars: 2 - Forks: 0
Jong-hun-Park/trviz
A python library for decomposing and visualizing tandem repeat sequences
Language: Python - Size: 2.64 MB - Last synced at: 19 days ago - Pushed at: over 1 year ago - Stars: 10 - Forks: 1
d-dawg78/COMP561-Final-Project
McGill University - Computational Biology Methods and Research Project
Language: Python - Size: 946 KB - Last synced at: about 2 months ago - Pushed at: about 4 years ago - Stars: 3 - Forks: 0
trishume/seqalign_pathing
Rust implementation of sequence alignment / Levenshtein distance by A* acceleration of the DP algorithm
Language: Rust - Size: 5.86 KB - Last synced at: 9 days ago - Pushed at: almost 8 years ago - Stars: 21 - Forks: 3
thekaplanlab/msabrowser
🧬 MSABrowser: dynamic and fast visualization of sequence alignments, variations, and annotations
Language: JavaScript - Size: 412 KB - Last synced at: 6 months ago - Pushed at: about 1 year ago - Stars: 31 - Forks: 7
TravisWheelerLab/polyA
Automatically Adjudicate Any And All Arbitrary Annotations, Astutely Adjoin Abutting Alignments, And Also Amputate Anything Amiss (AAAAAAAAAAAAAAAA)
Language: Python - Size: 59 MB - Last synced at: 9 days ago - Pushed at: about 1 year ago - Stars: 8 - Forks: 2
salilab/salign
Web service for multiple protein sequence/structure alignment
Language: Perl - Size: 524 KB - Last synced at: 7 months ago - Pushed at: 8 months ago - Stars: 0 - Forks: 0
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: VHDL - Size: 21.2 MB - Last synced at: 7 months ago - Pushed at: about 2 years ago - Stars: 48 - Forks: 11
LKremer/MSA_trimmer
Straightforward & minimalistic removal of poorly aligned regions in sequence alignments.
Language: Python - Size: 8.79 KB - Last synced at: 24 days ago - Pushed at: about 6 years ago - Stars: 17 - Forks: 2
SUGAM2001/Python-for-Bioinformatics
A collection of python script, books, and tutorials for bioinformatics.
Language: Python - Size: 18.1 MB - Last synced at: 9 months ago - Pushed at: 9 months ago - Stars: 0 - Forks: 0
lisabensoussan/DNA_lab
This project provides hands-on experience in DNA analysis using R, covering sequence manipulation, mutation analysis, GC content, fragment analysis, sequence alignment, RNA-seq, variant analysis, and phylogenetics.
Language: HTML - Size: 6.51 MB - Last synced at: 3 months ago - Pushed at: 9 months ago - Stars: 0 - Forks: 0
phylogeny-lab/phylogeny-lab
A phylogenetics web app
Language: TypeScript - Size: 5.56 MB - Last synced at: 9 months ago - Pushed at: 9 months ago - Stars: 0 - Forks: 0
