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Search results for bioinformatics sequence alignment
bioinformatics
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sequence-alignment
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49 search results found
Biopython
⭐
3,918
Official git repository for Biopython (originally converted from CVS)
Minimap2
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1,613
A versatile pairwise aligner for genomic and spliced nucleotide sequences
Bwa
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1,282
Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)
Jcvi
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650
Python library to facilitate genome assembly, annotation, and comparative genomics
Bwa Mem2
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645
The next version of bwa-mem
Vsearch
⭐
605
Versatile open-source tool for microbiome analysis
Biojava
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564
📖🔬☕ BioJava is an open-source project dedicated to providing a Java library for processing biological data.
Edlib
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421
Lightweight, super fast C/C++ (& Python) library for sequence alignment using edit (Levenshtein) distance.
Seqan3
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373
The modern C++ library for sequence analysis. Contains version 3 of the library and API docs.
Minigraph
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367
Proof-of-concept seq-to-graph mapper and graph generator
Sequenceserver
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259
Intuitive graphical web interface for running BLAST bioinformatics tool (i.e. have your own custom NCBI BLAST site!)
Miniprot
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231
Align proteins to genomes with splicing and frameshift
Ksw2
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115
Global alignment and alignment extension
Buddysuite
⭐
105
Bioinformatics toolkits for manipulating sequence, alignment, and phylogenetic tree files
Kalign
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105
A fast multiple sequence alignment program.
Cogent3
⭐
79
Comparative Genomics Toolkit 3
Pymod
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61
PyMod 3 - sequence similarity searches, multiple sequence/structure alignments, and homology modeling within PyMOL.
Biscuit
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61
BISulfite-seq CUI Toolkit
Uta
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59
Universal Transcript Archive: comprehensive genome-transcript alignments; multiple transcript sources, versions, and alignment methods; available as a docker image
Arioc
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54
Arioc: GPU-accelerated DNA short-read alignment
Microbetrace
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53
The Visualization Multitool for Molecular Epidemiology and Bioinformatics
Bioalignments.jl
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51
Sequence alignment tools
Unimap
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49
A fork of minimap2 optimized for assembly-to-reference alignment
Minimap2 Rs
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46
Rust bindings to minimap2 library
Pymsaviz
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41
MSA(Multiple Sequence Alignment) visualization python package for sequence analysis
Sequence_align
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39
Efficient implementations of Needleman-Wunsch and other sequence alignment algorithms written in Rust with Python bindings via PyO3.
Miniwfa
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37
A reimplementation of the WaveFront Alignment algorithm at low memory
Rdptools
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36
Collection of commonly used RDP Tools for easy building
Ema
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30
Fast & accurate alignment of barcoded short-reads
Bioseq Js
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30
For live demo, see http://lh3lh3.users.sourceforge.net/bioseq.shtml
Orthoevolution
⭐
28
An easy to use and comprehensive python package which aids in the analysis and visualization of orthologous genes. 🐵
Awesome Sequencing Tech Papers
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26
A collection of publications on comparison of high-throughput sequencing technologies.
Opal
⭐
24
SIMD C/C++ library for massive optimal sequence alignment (local/SW, infix, overlap, global)
Wfa Gpu
⭐
24
GPU implementation of the Wavefront Alignment Algorithm for global, gap-affine, pairwise sequence alginment
Sina
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24
SINA - Reference based multiple sequence alignment
Msabrowser
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21
🧬 MSABrowser: dynamic and fast visualization of sequence alignments, variations, and annotations
Rnaseq Pipeline
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18
RNA-seq pipeline for raw sequence alignment and transcript/gene quantification.
Pyfamsa
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17
Cython bindings and Python interface to FAMSA, an algorithm for ultra-scale multiple sequence alignments.
Nucleic Acid
⭐
15
BWT, FM-index and bits vector for analyzing DNA sequence data.
Biomsalign
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15
JavaScript library for Multiple Sequence Alignment
Lexicon Mono Seq
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13
DOM Text Based Multiple Sequence Alignment Library
Pymuscle5
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12
Cython bindings and Python interface to MUSCLE v5, a highly efficient and accurate multiple sequence alignment software.
Genome On Diet
⭐
11
Genome-on-Diet is a fast and memory-frugal framework for exemplifying sparsified genomics for read mapping, containment search, and metagenomic profiling. It is much faster & more memory-efficient than minimap2 for Illumina, HiFi, and ONT reads. Described by Alser et al. (preliminary version: https://arxiv.org/abs/2211.08157).
Genomics Workspace
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11
Django website project for common sequence search tools.
Sigalign
⭐
10
A Similarity-Guided Alignment Algorithm
Positive Selection
⭐
10
Scripts and procedures for detecting positively selected genes and codons in primates
Polya
⭐
7
Automatically Adjudicate Any And All Arbitrary Annotations, Astutely Adjoin Abutting Alignments, And Also Amputate Anything Amiss (AAAAAAAAAAAAAAAA)
Mummergpu
⭐
7
Fork of MUMmerGPU-2.0 that compiles without errors
Teacheng
⭐
6
A Teaching Engine for Genomics
Ebt
⭐
6
Evolutionary Bioinformatics Toolkit (EBT)
Pyopal
⭐
6
Cython bindings and Python interface to Opal, a SIMD-accelerated database search aligner.
Microbetrace
⭐
5
The Visualization Multitool for Molecular Epidemiology and Bioinformatics
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