I would like to obtain the hydropathy plots of several aligned protein sequences and display them in a similar manner to this BMC Evolutionary Biology paper
They state that they used EMBOSS pepwindowall (a web version is also available), but while that program is able to output several sequences it gets very messy since one cannot display each sequence analysed with a different colour. I have tried to locate alternative programs, but have failed so far.
I hope I do not have to perform separate runs, colour each using Photoshop and then overlay them ;)
all the best,