PoincaréMSA is a computational tool for visualization of large protein families developed by Susmelj et al. PoincaréMSA builds an interactive projection of an input protein multiple sequence alignment provided by the user or built on-the-flow from the target sequence. The underlying algorithm is based on Poincaré maps introduced by Klimovskaia et al.. It successfully reproduces both local proximities between protein sequences as well as global hierarchical structure of the data.
You can find a step-by-step explication of PoincaréMSA construction on the "Tutorial" page and several examples of PoincaréMSA projection for protein families on the "Examples" page. The source code is available at https://github.com/DSIMB/PoincareMSA.
Please use the following reference when citing the PoincaréMSA:
Susmelj A.K., Ren Y., Vander Meersche Y., Gelly J.C., & Galochkina T. (2023). Poincaré maps for visualization of large protein families. Briefings in bioinformatics, -. https://doi.org/10.1093/bib/bbad103
.mfastaformat provided by a user. The user can also provide an annotation in
.csvformat which will be used for coloring, as well as an UniProt IDs list used to automatically fetch taxonomy informations.