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Search results for sequence alignment

sequence-alignment x

129 search results found

Biopython ⭐ 3,918

Official git repository for Biopython (originally converted from CVS)

Minimap2 ⭐ 1,613

A versatile pairwise aligner for genomic and spliced nucleotide sequences

Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)

Diamond ⭐ 900

Accelerated BLAST compatible local sequence aligner.

Python library to facilitate genome assembly, annotation, and comparative genomics

Bwa Mem2 ⭐ 645

The next version of bwa-mem

Vsearch ⭐ 605

Versatile open-source tool for microbiome analysis

Biojava ⭐ 564

📖🔬☕ BioJava is an open-source project dedicated to providing a Java library for processing biological data.

SeqAn's official repository.

Lightweight, super fast C/C++ (& Python) library for sequence alignment using edit (Levenshtein) distance.

The modern C++ library for sequence analysis. Contains version 3 of the library and API docs.

Minigraph ⭐ 367

Proof-of-concept seq-to-graph mapper and graph generator

Bistring ⭐ 360

Bidirectionally transformed strings

Sequenceserver ⭐ 259

Intuitive graphical web interface for running BLAST bioinformatics tool (i.e. have your own custom NCBI BLAST site!)

Miniprot ⭐ 231

Align proteins to genomes with splicing and frameshift

Modular BioJS compoment for a multiple sequence alignment

🚥 Visualizing publication-quality multiple sequence alignment using ggplot2

C++ htslib/bwa-mem/fermi interface for interrogating sequence data

Global alignment and alignment extension

Buddysuite ⭐ 105

Bioinformatics toolkits for manipulating sequence, alignment, and phylogenetic tree files

A fast multiple sequence alignment program.

abPOA: an SIMD-based C library for fast partial order alignment using adaptive band

Inference of couplings in proteins and RNAs from sequence variation

Deepsequence ⭐ 83

A generative latent variable model for biological sequence families.

Deepblast ⭐ 80

Neural Networks for Protein Sequence Alignment

Comparative Genomics Toolkit 3

Snp Dists ⭐ 68

Pairwise SNP distance matrix from a FASTA sequence alignment

Orthologr ⭐ 68

Genome wide orthology inference and dNdS estimation

BISulfite-seq CUI Toolkit

PyMod 3 - sequence similarity searches, multiple sequence/structure alignments, and homology modeling within PyMOL.

Universal Transcript Archive: comprehensive genome-transcript alignments; multiple transcript sources, versions, and alignment methods; available as a docker image

Arioc: GPU-accelerated DNA short-read alignment

Microbetrace ⭐ 53

The Visualization Multitool for Molecular Epidemiology and Bioinformatics

Bioalignments.jl ⭐ 51

Sequence alignment tools

Viralmsa ⭐ 50

Reference-guided multiple sequence alignment of viral genomes

A fork of minimap2 optimized for assembly-to-reference alignment

Minimap2 Rs ⭐ 46

Rust bindings to minimap2 library

Exonerate ⭐ 45

A generic tool for sequence alignment

Gremlin_cpp ⭐ 45

GREMLIN - learn MRF/potts model from input multiple sequence alignment! Implementation now available in C++ and Tensorflow/Python!

Sneakysnake ⭐ 44

SneakySnake🐍 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.

a multiple sequence alignment-trimming algorithm for accurate phylogenomic inference

Pymsaviz ⭐ 41

MSA(Multiple Sequence Alignment) visualization python package for sequence analysis

Scalable long read self-correction and assembly polishing with multiple sequence alignment

Sequence_align ⭐ 39

Efficient implementations of Needleman-Wunsch and other sequence alignment algorithms written in Rust with Python bindings via PyO3.

A reimplementation of the WaveFront Alignment algorithm at low memory

Rdptools ⭐ 36

Collection of commonly used RDP Tools for easy building

Blast Bioinfor Tool ⭐ 30

Python implementation of Basic Local Alignment Search Tool (BLAST) , which is the core algorithm in sequence alignment for genomes.

Fast & accurate alignment of barcoded short-reads

Bioseq Js ⭐ 30

For live demo, see http://lh3lh3.users.sourceforge.net/bioseq.shtml

Python Alignment ⭐ 30

Native Python library for generic sequence alignment

sequence alignment. global, local, glocal.

Orthoevolution ⭐ 28

An easy to use and comprehensive python package which aids in the analysis and visualization of orthologous genes. 🐵

Banded Striped DNA Sequence Alignment

Awesome Sequencing Tech Papers ⭐ 26

A collection of publications on comparison of high-throughput sequencing technologies.

mdciao: Analysis of Molecular Dynamics Simulations Using Residue Neighborhoods

Pdbcolor ⭐ 24

Python code to color a PDB structure based on parameters from a multiple sequence alignment

SINA - Reference based multiple sequence alignment

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

Phylotar ⭐ 24

An automated pipeline for retrieving orthologous DNA sequences from GenBank in R

SIMD C/C++ library for massive optimal sequence alignment (local/SW, infix, overlap, global)

Bioinf2019 ⭐ 23

Msabrowser ⭐ 21

🧬 MSABrowser: dynamic and fast visualization of sequence alignments, variations, and annotations

MARS: improving Multiple circular sequence Alignment using Refined Sequences

Macse_v2_pipelines ⭐ 21

This repository provides source code for several pipelines dedicated to the alignment of nucleotide coding sequences that are based on MACSE. These pipelines are mostly bash scripts encapsulated within singularity containers and sometimes combined in nextflow workflows.

Rnaseq Pipeline ⭐ 18

RNA-seq pipeline for raw sequence alignment and transcript/gene quantification.

Tredparse ⭐ 17

TREDPARSE: HLI Short Tandem Repeat (STR) caller

Cython bindings and Python interface to FAMSA, an algorithm for ultra-scale multiple sequence alignments.

Contact Prediction ToolKit

Chromeister ⭐ 16

A dotplot generator for large chromosomes

Alignmentviewer ⭐ 15

Multiple sequence alignment visualizer

Biomsalign ⭐ 15

JavaScript library for Multiple Sequence Alignment

AIM, A Framework for High-throughput Sequence Alignment using Real Processing-in-Memory Systems, Bioinformatics, btad155, https://doi.org/10.1093/bioinformatics/btad155

Nucleic Acid ⭐ 15

BWT, FM-index and bits vector for analyzing DNA sequence data.

Seqalign ⭐ 14

Collection of sequence alignment algorithms.

genomic alignment similarity search tool

Lexicon Mono Seq ⭐ 13

DOM Text Based Multiple Sequence Alignment Library

EMERALD calculates safety-windows by exploring the suboptimal alignment space

Pymuscle5 ⭐ 12

Cython bindings and Python interface to MUSCLE v5, a highly efficient and accurate multiple sequence alignment software.

Seqalign_pathing ⭐ 12

Rust implementation of sequence alignment / Levenshtein distance by A* acceleration of the DP algorithm

R package for multiple sequence alignment

Homoplasyfinder ⭐ 12

A tool to identify and annotate homoplasies on a phylogeny and sequence alignment

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 ⭐ 11

Django website project for common sequence search tools.

Raxml_ascbias ⭐ 11

Script for removing or counting invariant sites for the RAxML ascertainment bias corrections

Positive Selection ⭐ 10

Scripts and procedures for detecting positively selected genes and codons in primates

Redotable ⭐ 10

A dotplot application for DNA/RNA sequence

Fast pairwise sequence alignment using SeqAn, in Python.

abPOA: an SIMD-based C library for fast partial order alignment using adaptive band

Spacepile ⭐ 10

convert reads from repeated measures of same piece of DNA into spaced matricies for deep learners.

Sigalign ⭐ 10

A Similarity-Guided Alignment Algorithm

Processing Dynamicprogramming ⭐ 9

An implementation of the Dynamic Programming optimized search technique as well as a series of applications that take advantage of it such as image seam carving and textual sequence alignment.

Needleman Wunsch ⭐ 9

An implementation of the Needleman-Wunsch global alignment algorithm in PHP

GSAlign: an ultra-fast sequence alignment algorithm for intra-species genome comparison

Sanskrit Alignment ⭐ 9

Sequence alignment and textual reconstruction for Sanskrit texts

Function Merging & Branch Fusion

Genopo a.k.a. F5N - A nanopore sequencing analysis toolkit for Android smartphones https://nanoporetech.com

BLAST-Like Alignment Tool

Tmscoring ⭐ 8

Python implementation of the TMscore program

Vectorian ⭐ 8

A search engine for intertextual references based on sequence alignments of word embeddings

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