Top 4 C++ sequence-alignment Projects

diamond

3 954 6.3 C++

Accelerated BLAST compatible local sequence aligner. (by bbuchfink)

Project mention: comparing the similarity between a set of protein sequences | /r/genomics | 2023-05-12

Diamond (https://github.com/bbuchfink/diamond) might help. It has a protein sequence clustering option. You could cluster your sequences and then take the centroids of each cluster. Vary the BLAST parameters to increase/decrease the numbers of clusters.

bwa-mem2

2 676 2.6 C++

The next version of bwa-mem
WorkOS

workos.com sponsored

The modern identity platform for B2B SaaS. The APIs are flexible and easy-to-use, supporting authentication, user identity, and complex enterprise features like SSO and SCIM provisioning.
edlib

2 484 1.1 C++

Lightweight, super fast C/C++ (& Python) library for sequence alignment using edit (Levenshtein) distance.
seqan3

1 386 8.9 C++

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

NOTE: The open source projects on this list are ordered by number of github stars. The number of mentions indicates repo mentiontions in the last 12 Months or since we started tracking (Dec 2020).