SLiMSuite and SeqSuite have grown into rather unwieldy beasts since their origins as individual programs and the documentation has struggled to keep up. In particular, the original plan of a single PDF manual per program is getting creaky. Because of the shared reliance on common modules, multiple programs make use of the same sets of options for alignments and conservation scoring etc. and propagating tweaks and modifications through all the manuals can be a bit head-wrecking.
As a result of all of this, the documentation currently undergoing a bit of a review and rethink. I am still keen to keep the PDF manuals (as I think they are useful) but will be working through an intermediate phase of online Markdown/HTML documentation of some kind. The current plan is to trickle out draft copies via the blog and then probably release a Git repository once sufficiently populated.
In the meantime, I would be interested to hear any thoughts regarding favoured documentation styles etc. (e.g. HTML vs PDF, large files vs small chunks) as well as bits that are particularly unclear or in need of attention.