The EMBASSY packages include applications with the same look and feel as EMBOSS applications, but which are kept separate from EMBOSS. This is usually because the packages are for specialised sequence analysis, or for non-sequence based analysis, or are licensed differently from EMBOSS (i.e. non-GPL), or done so at the author's request.
The EMBASSY packages currently include:
PHYLIPNEW (now phylip 3.68)
Also, various packages for protein structure and related areas: