sequence-alignment

There are 24 repositories under sequence-alignment topic.

biopython / biopython
Official git repository for Biopython (originally converted from CVS)
bioinformatics biopython dna genomics phylogenetics protein protein-structure python sequence-alignment
Language:Python 4806
lh3 / minimap2
A versatile pairwise aligner for genomic and spliced nucleotide sequences
bioinformatics genomics sequence-alignment spliced-alignment
Language:C 2069
lh3 / bwa
Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)
bioinformatics fm-index genomics sequence-alignment
Language:C 1672
bbuchfink / diamond
Accelerated BLAST compatible local sequence aligner.
sequence-alignment
Language:C++ 1199
bwa-mem2 / bwa-mem2
The next version of bwa-mem
bioinformatics genomics sequence-alignment
Language:C++ 792
torognes / vsearch
Versatile open-source tool for microbiome analysis
amplicon bioinformatics chimera clustering fasta fastq metabarcoding metagenomics microbiome search sequence-alignment
Language:C++ 724
biojava / biojava
:book::microscope::coffee: BioJava is an open-source project dedicated to providing a Java library for processing biological data.
bioinformatics java protein-structure genomics protein-sequences protein-modification sequence-alignment structure-alignment protein-data-bank pdb parser-library structural-bioinformatics
Language:Java 616
Martinsos / edlib
Lightweight, super fast C/C++ (& Python) library for sequence alignment using edit (Levenshtein) distance.
alignment-path bioinformatics c-plus-plus edit-distance levehnstein-distance library python sequence-alignment
Language:C++ 570
lh3 / minigraph
Sequence-to-graph mapper and graph generator
bioinformatics genomics sequence-alignment genome-graph pan-genome
Language:C 459
seqan3
seqan / seqan3
The modern C++ library for sequence analysis. Contains version 3 of the library and API docs.
sequence-analysis seqan cpp20 cpp-concepts bioinformatics blast sequence-alignment fasta fastq samtools fm-index modern
Language:C++ 441
lh3 / miniprot
Align proteins to genomes with splicing and frameshift
bioinformatics sequence-alignment
Language:C 383
microsoft / bistring
Bidirectionally transformed strings
string sequence-alignment
Language:Python 370
wurmlab / sequenceserver
Intuitive graphical web interface for running BLAST bioinformatics tool (i.e. have your own custom NCBI BLAST site!)
bioinformatics blast genomics genomics-visualization hacktoberfest javascript ruby sequence-alignment sequencing visualization
Language:JavaScript 289
shenwei356 / LexicMap
LexicMap: efficient sequence alignment against millions of prokaryotic genomes
prokaryotic-genomes sequence-alignment sequence-search alignment large-scale-dataset microbial-genomes bacterial-database bacterial-genomes lexichash
Language:Go 197
pyMSAviz
moshi4 / pyMSAviz
MSA(Multiple Sequence Alignment) visualization python package for sequence analysis
bioinformatics genomics matplotlib msa multiple-sequence-alignment python sequence-alignment sequence-analysis visualization
Language:Python 157
TimoLassmann / kalign
A fast multiple sequence alignment program.
bioinformatics sequence-alignment sequence-analysis
Language:C 147
lh3 / ksw2
Global alignment and alignment extension
sequence-alignment bioinformatics
Language:C 139
cogent3 / cogent3
Comparative Genomics Toolkit 3
bioinformatics pycogent statistics data-science biology genomics evolution biopython markov-chain molecular-evolution non-stationary phylogenetic-trees phylogenetics python parallel signal-processing maximum-likelihood biological-sequence-analysis sequence-alignment
Language:Python 133
flatironinstitute / deepblast
Neural Networks for Protein Sequence Alignment
language-modeling neural-networks protein protein-sequences protein-structure sequence-alignment structural-alignments
Language:Python 131
jguhlin / minimap2-rs
Rust bindings to minimap2 library
alignment bioinformatics ffi longread minimap2 rust genomics sequence-alignment spliced-alignment
Language:Jupyter Notebook 101
drostlab / orthologr
Genome wide orthology inference and dNdS estimation
blast-searches orthology-inference comparative-genomics-studies genomics sequence-alignments blast comparative dnds-estimation codon-alignment r entire-genomes orthologous-genes biomartr species comparing-genomes genomics-studies retrieve-genomes comparative-genomics proteome sequence-alignment
Language:R 96
MicrobeTrace
CDCgov / MicrobeTrace
The Visualization Multitool for Molecular Epidemiology and Bioinformatics
bioinformatics epidemiology network-visualization hiv cdc pathogens phylogenetics phylogenetic-trees phylogeny phylogenomics genomics genomics-visualization genomic-data-analysis sequence-alignment nchhstp nchhstp-dhp
Language:TypeScript 95
lh3 / unimap
A EXPERIMENTAL fork of minimap2 optimized for assembly-to-reference alignment
bioinformatics genomics sequence-alignment
Language:C 87
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 74
biocommons / uta
Universal Transcript Archive: comprehensive genome-transcript alignments; multiple transcript sources, versions, and alignment methods; available as a docker image
bioinformatics sequences sequence-alignment
Language:Python 71
RWilton / Arioc
Arioc: GPU-accelerated DNA short-read alignment
bioinformatics genomics read-aligners sequence-alignment dna-sequence-alignment gpu bisulfite-sequencing methylation cuda c-plusplus variant-analysis
70
zhou-lab / biscuit
BISulfite-seq CUI Toolkit
bioinformatics dna-methylation sequence-alignment
Language:C 68
BioJulia / BioAlignments.jl
Sequence alignment tools
bam-files sam-files sequence-alignment sequence-analysis dna-sequences biology bioinformatics smith-waterman-alignment high-throughput-sequencing biojulia
Language:Julia 64
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 53
rdpstaff / RDPTools
Collection of commonly used RDP Tools for easy building
16s bioinformatics microbiome microbiology bayesian-classifiers sequence-alignment
Language:Makefile 51
nahmedraja / GASAL2
sequence-alignment gpu-acceleration cuda-library bioinfomatics
Language:C++ 50
lh3 / miniwfa
A reimplementation of the WaveFront Alignment algorithm at low memory
bioinformatics sequence-alignment
Language:C 49
ITBE-Lab / MA
The Modular Aligner and The Modular SV Caller
alignment bioinformatics sequence-alignment read-aligners fm-index structural-variation seeds
Language:C++ 46
estebanpw / chromeister
A dotplot generator for large chromosomes
dotplot chromosomes genome genome-comparisons genomics sequence-alignment plants fast lightweight
Language:C 43
lh3 / bioseq-js
For live demo, see http://lh3lh3.users.sourceforge.net/bioseq.shtml
bioinformatics sequence-alignment
Language:HTML 39
Martinsos / opal
SIMD C/C++ library for massive optimal sequence alignment (local/SW, infix, overlap, global)
sequence-alignment bioinformatics smith-waterman c-plus-plus avx alignment database-search
Language:C++ 39