SortMeRNA: next-generation sequence filtering and alignment tool

elPrep: a high-performance tool for analyzing sequence alignment/map files in sequencing pipelines.

Tools for manipulating biological data, particularly multiple sequence alignments

A collection of tools for Multiple Alignments of DNA, RNA, Protein Sequence

Goalign is a set of command line tools and an API to manipulate multiple sequence alignments. It is implemented in Go language.

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

A fork of exonerate: a generic tool for sequence alignment

Sequence alignment tools

Tool to flag foldback and chimeric artifacts in long-read sequence alignment files

High throughput tool for tall and wide multiple sequence alignment.

Reverse engineering tool using bioinformatics sequence alignment algorithms

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

Jupiter Bioinformatics is a browser-based tool for interactive pairwise sequence alignment and heatmap visualization. Built on the Smith-Waterman local alignment algorithm, it renders the full scoring matrix as a color-coded heatmap on an HTML5 canvas, no installation, no server, no dependencies. Open the file and start aligning.

A tool for visualization of pairwise alignments of multiple sequences

Pacbio sequence alignment tool, please use "git clone" to copy and use the repository

A DIY Guide To BLAST Tools For Sequence Alignment

A sequence alignment tool

Tool for exploring sequence alignment algorithms

Interface to Popular Multiple Sequence Alignment Tools - R-package

Basic Local Alignment and Search Tool for Oxford Nanopore Long Sequences

ProGraphMSA is a state-of-the-art multiple sequence alignment tool which produces phylogenetically sensible gap patterns while maintaining robustness by allowing alternative splicings and errors in the branching pattern of the guide tree. Fork of ProGraphMSA+TR from https://sourceforge.net/projects/prographmsa

a tools that implements an algorithm for optimal alignment of sequences with structural variants (SVs)

Tools for sequence and alignment manipulation

comb aligner -- a graphical nucleotide sequence alignment tool

A simple visualisation tool for Multiple Sequence Alignment.

A tool for the statistical comparison of alternative multiple sequence alignments

⚙️TPMA: a two pointers meta-alignment tool to ensemble different nucleic acid multiple sequence alignment results

msaconverter is a tool to convert a multiple sequence alignment into different format with Biopython (http://www.biopython.org/)

An alignment-independent tool for the study of pathogen sequence diversity

A compositional bias testing and pruning tool for multiple sequence alignments