Dear Olivier,

HyPhy uses the standard IUPAC (Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login) table to deal with ambiguities (in nucleotide data). All of those are understood and analyzed. See a section in the first chapter of my disseration Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login for exact details. HyPhy is NOT case sesnsitive.

If an unknown charater is encountered, it is ignored in that sequence only. You can also augment the standard table to deal with any character you like. This can be done directly in the datafile, by including an appropriate header.

Cheers,
Sergei