Open-source alternatives to Diamond

Biopython is a bioinformatics library for Python providing tools to parse, manipulate, and analyze biological sequences, molecular structures, and phylogenetic trees. It serves as a biological sequence parser for genomic and proteomic data across multiple industry-standard file formats and acts as an interface for querying biological data and citations from NCBI Entrez repositories. The project distinguishes itself through specialized toolkits for protein structure analysis and phylogenetic tree construction. It includes a protein structure analyzer for processing PDB and mmCIF files to calcu

klib is a comprehensive C standard library extension and data structure toolkit. It provides a set of fundamental tools for memory management, data organization, and general-purpose utility functions for standalone C applications. The project features specialized capabilities for bioinformatics sequence analysis, including the parsing of FASTA, FASTQ, and Newick formats and the implementation of Smith-Waterman sequence alignment and Hidden Markov Models. It also includes a mathematical computation library for numerical routines and expression evaluation, as well as a lightweight HTTP and FTP

Pairwise Sequence Alignment Library

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