biology/phyml: fix build on non-x86

• only initialise x86-only fields on x86.
• make code compatible with platforms where char is unsigned

Obtained from: https://github.com/stephaneguindon/phyml/commit/9c55b683c875fb9923e7cb2a1092596f72040882
MFH: 2023Q2

(cherry picked from commit 8e2ec289a2d8891c9bd3c549319baa9c94cfda27)