>If I delete the 'embassy: "phylip"' line, it seems to work. >What am I doing wrong? This problem was caused by some unavoidable updates to the embassy applications between releases. The fix is to recompile emboss using the 'ajacd.c' file in the: ftp://ftp.hgmp.mrc.ac.uk/pub/EMBOSS/patchfiles/ directory. HTH Alan