Aligners find the similarity between two or more sequences. Sometimes, query sequences are compared against a reference database in a sort of fuzzy search (e.g. Bowtie 2). In other contexts, several query sequences are compared against one another (e.g. Clustal Omega).
Most aligners are tailored for specific types of data: STAR for single-cell RNA-Seq, DIAMOND BLASTP for protein sequences against a protein database, and DIAMOND BLASTX for translated nucleotide sequences against a protein database.
Toolchest hosts both the aligner and the reference databases, and you can also use your own custom database.
If you don't need the extra information that aligners return – e.g. for some microbiome taxonomic classification – you can also use a more efficient classifier.
If you want to use an aligner that's not listed here, let us know! It might already be available on our infrastructure but not documented.