- Wasabi, visualisation of rich MSAs and graphical interface to command-line programs: http://wasabiapp.org.
- PRANK, phylogeny-aware alignment of DNA, codon and amino-acid sequences: http://wasabiapp.org/software/prank.
- PAGAN, phylogeny-aware sequence alignment and alignment extension: http://wasabiapp.org/software/pagan.
- FPA, alignment with template switching: https://github.com/ariloytynoja/fpa.
- Séance, community analysis of 18S rRNA marker gene data: http://wasabiapp.org/software/seance.
- Canopy, iterative co-estimation of tree and MSA: http://wasabiapp.org/software/canopy.
- Archive of old software.