Documentation patches

[Benjamin Redelings]

Hi Karolis,

I pushed a few fixes to the version-3 branch.  If you make a
pull-request with documentation fixes, probably the best thing to do
would be to make the PR against the master branch, and then I will copy
those changes into the version-3 branch.  After enough fixes have
accumulated, I will tag 3.7.0 from the version-3 branch.

I can also make github compile pre-releases for testing.  Right now the
only prerelease is 4.0-alpha1, but it should also be possible to make
e.g. a 3.7.0-beta1 prerelease.

-BenRI

[Karolis Ramanauskas]

PR created. Hopefully, I didn't mess up anything. I used a Mac (case-insensitive file system), and noticed this:

'tests/data/Primates.nex'

'tests/data/primates.nex'

Karolis