Active software development projects:
- Twitcher and Twitcher Workbench, analysis and annotation of template switch mutations: https://twitcher.it.helsinki.fi
Some of the research software developed in the group:
- Wasabi, visualisation of rich MSAs and graphical interface to command-line programs: https://github.com/veidenberg/wasabi
- PRANK, phylogeny-aware alignment of DNA, codon and amino-acid sequences: https://ariloytynoja.github.io/prank-msa.
- PAGAN, phylogeny-aware sequence alignment and alignment extension: https://ariloytynoja.github.io/pagan-msa.
- FPA, alignment with template switching: https://github.com/ariloytynoja/fpa.
- Séance, community analysis of 18S rRNA marker gene data: https://github.com/ariloytynoja/seance.
- Canopy, iterative co-estimation of tree and MSA: https://github.com/ariloytynoja/canopy.
- Legacy code for ProAlign: https://github.com/ariloytynoja/ProAlign.