Dear Becky,
I have identified some problems with my NEXUS reader which caused your file to be rejected.
Specifically, your file had the following NEXUS block:
Code:BEGIN DATA;
dimensions ntax=189 nchar=1620;
format missing=?
symbols="ABCDEFGHIKLMNPQRSTUVWXYZ"
datatype=DNA interleave gap= -;
HyPhy expected the symbols command to contain characters separated by a space (e.g. "ABC..." should be "A B C..."). I looked at the NEXUS format specification and realized that this was actually not necessary, but that "ABC..." is acceptable. This has been fixed in today's build.
Also, HyPhy had a bug which cause the 'gap= -' to be interpreted incorrectly, because of the space after '='. This has also been fixed.
You can either download the new version, or modify the header to read:
Code:BEGIN DATA;
dimensions ntax=189 nchar=1620;
format missing=?
datatype=DNA interleave gap=-;
Note that the SYMBOLS command actually defines a new character alphabet, and your data will not be interpreted as DNA. In the original header, the DNA datatype will over-ride the symbols command. I am pretty sure that SYMBOLS is inappropriate in this context and is incorrectly output. As written, the block implies that all listed characters (not just ACGT) are valid DISTINCT states, whereas in reality they should be defined ambiguities. At any rate, I would advise you to remove the SYMBOLS statement altogether.
Cheers,
Sergei