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PRALINE 2 is a toolkit for custom multiple sequence alignment workflows. It can be used to incorporate sequence annotations, such as secondary structure or (DNA) motifs, into the alignment scoring, as well as to customize many other aspects of a progressive multiple alignment workflow. PRALINE 2 is implemented in Python and available as open source software on GitHub: https://github.com/ibivu/PRALINE/.doi:10.1093/bioinformatics/btz572 pmid:31368486 pmcid:PMC6954659 fatcat:piru5evktjdkhdtmp5d4rvbucy