Trainers and patches come in three forms: IPS, XDelta and BSDiff.
GBA patches will favour ips format however with DS bing a mixture of the three types listed.
Once you patched the roms (you patch before you write) burn as usual, you can usually do any fiddling with the rom as well (I dropped the intro to castlevania after patching).
XDelta: XDelta download page That version is for windows although it originally was a linux app and I believe there is a mac version around somewhere as well.
The syntax is as follows xdelta patch (patchname) (original file) output file)
Here is the command line I gave with my NSMB translations:
With regard to a GUI the NINJA2.0 betas had a kind of frontend (you needed the xdelta app in the same dir) but things are a bit hazy regarding its present state: http://ninja.cinnamonpirate.com/
BSDiff (a lot of the release group made trainers): Here is a batch file I made for the sonic rush trainer
simply put it goes bspatch original.file new.file patch.bdf
You may also need a copy of bspatch (the trainers came with it but GBATemp removed the exe files from the archive):
http://sites.inka.de/tesla/f_others.html#bsdiff
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