TriFusion is a modern GUI and command line application designed to make the life of anyone with proteome and/or alignment sequence data easier and more pleasurable. It allows user to process their data through three independent modules: (i) Search and explore orthologs across multiple proteomes; (ii) Convert, concatenate, collapse, filter and perform many other manipulations of thousands sequence alignments files. (iii) Visually explore your sequence alignment data with dozens of graphical and statistical options that generate publication ready graphics. Regardless of your experience in bioinformatics, TriFusion is easy to use and offers a wide array of powerful features to help you deal with your data. It is available for everyone on Windows, MacOS and Linux.