Ari Loytynoja University of Helsinki We have developed PAGAN, a new program for phylogeny-aware multiple sequence alignment using partial-order sequence graphs, and Wasabi, a graphical front-end for phylogeny-aware alignment. In PAGAN, we use sequence graphs to model uncertainties in character presence/absence and thus make the phylogeny-aware algorithm less sensitive to errors in guide phylogeny or noisy input data. In addition to de novo alignment, PAGAN can extend existing alignments with new data: we have built applications of this for phylogenetic placement of marker gene data and for reference-based scaffolding of NGS data. Phylogeny-aware alignment tightly couples the alignment with the underlying guide phylogeny and provides e.g. inferred ancestral sequences associated with the internal tree nodes. We built Wasabi to display these information and to provide a user-friendly access to PAGAN and other tools. PAGAN and Wasabi are available at http://wasabiapp.org.