Phonology of Voynichese

[MarcoP]

Hi Emma, 
the way in which e,a,o,y differ from the other glyphs appears to be the clearest "phonological" fact. I agree that it is reassuring that several different methods arrive at the same result in this case.

Part of the problem with 'i' was an error in my EVA mapping: CUVA G corresponds to EVA:g (not EVA:il, I got confused with Currier's transcription which appears in the same table as CUVA on You are not allowed to view links. Register or Login to view.). I apologize. I have now updated the graph.
It is still bizarre to see 'q' clustered with 'in', but at least all 'i's are still together at level 3.

Ah, I see! But, as you say, it's interesting that not only [q] but also [ch, sh], all of which tend toward the front of a word, cluster with [i] sequences which come at the end. Is the principle marking them as being in complementary distribution?

Hulden defines the obligatory contour principle (OCP) as "a universal cross-linguistic tendency to avoid redundancy or repetition of similar speech features within a word or morpheme, especially if the phonemes are adjacent to one another".
The principle is that characters that tend to occur consecutively must have different sounds, while characters with similar sounds never or very rarely appear next to each other. At the light of this, it seems clear why q- and -in end up being considered similar: they never appear in consecutive positions. Similarly, gallows do not appear consecutively, so they must be similar sounds. 
The positional constraints of Voynichese are so strong that they make several consecutive combinations impossible or very rare: this could contribute to make the lower splits in this tree unreliable (because they depend on ridiculously small numbers). On the other hand, some of those constraints may very well be a consequence of the OCP.