+ added full support for ambiguities present in the query sequences
!! This breaks compatibility for DBs built with previous versions. !!
+ ambiguities for nucleotides (R, Y, S, W, K, M, B, D, H, V, N, I, *, ., !)
+ ambiguities for amino acids (X, . )
+ phyml version is now explicitely tested before execution to ensure compatibility
- ambiguity support breaks compatibility with previous versions
- you do not anymore to define the states (-s) in placement phase, as this information is now saved in the database.
* ambiguity support will produce slightly different placement scores
* bugfix related to some phantom branch lengths that were incorrect
