Pyxel Edit is the best of the programs I've tried for seamless tiles. The others that I know of that do it don't do it quite as smoothly. Most of them do it by canvas wrap, so you can only work on one tile at a time, and sometimes the canvas wrap gets picky about where you try to draw across the edge. Pyxel Edit though, has a separate place for tiles and the canvas where you draw is also kind of a mapping editor. When you draw it will just let you draw with no worries about which spot is the "real" tile like in others. You can also draw on lots of tiles at once. This makes it really easy to get a mockup set up so you can see your tiles interacting with each other and edit any part of that mockup to look better. It also allows you to map those tiles in different orientations, so sometimes I'll use it just to work on magic circles or menu frames. The template I made isn't something that would make sense unless you drew on it inside of Pyxel Edit, then you could see how you're drawing in multiple places at once. If you're wanting to check it out, there is a much older version available for free, but be warned it is missing a lot of the current features and crashes often.
I'm still pretty new with Aseprite, so I don't know all of the things it can do. As far as I can tell it doesn't have any special functionality that other animation programs don't, but in my opinion it has a smoother workflow. I just find it a lot easier and faster to make smooth looking animations in than the others.
