linearize and simplify variation graphs using blocked partial order alignment

Identify long STRs, VNTRs, satellite DNA and other low-complexity regions in a genome

Global alignment and alignment extension

Pairwise whole genome aligner

Fast FASTA/Q parser and writer (C++ re-implementation of kseq library)

Red: an intelligent, rapid, accurate tool for detecting repeats de-novo on the genomic scale.

Program for aligning DNA sequences, a pairwise aligner.

modified from gitlab.com/manzai/Big-BWT to support fasta files

A compress suffix array built on prefix-free parsing.

Chimera: A Versatile Metagenomic Classification Tool

A fast, AVX2 and ARM Neon accelerated FM index library

Prefix Free Parsing

An optimal space run-length Burrows-Wheeler transform full-text index

Accelerating FM-index queries with PFP

Succinct Data Structure Library 2.0

BWT construction and search

Cache-friendly, Parallel, and Samplesort-based Constructor for Suffix Arrays and LCP Arrays

Hierarchical Alignment Format

Tools for manipulating sequence graphs in the GFA and rGFA formats

HAlign 4: A New Strategy for Rapidly Aligning Millions of Sequences

Accurate Species Tree EstimatoR: a family of optimation algorithms for species tree inference (including ASTRAL & CASTER)

Accurate Species TRee ALgorithm

Ribbit is a tool to identify tandem repeats in genome sequences.

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