Tested converting Mesquite character matrix to CipresIDL
matrix by comparing converted matrix with matrix obtained
from read_nexus_server.  mesquite.cipres.MesquiteCipresTypeConverter
invokes code to do the comparison when you run rec-i-dcm.  The 
comparison prompts you to enter the name of the nexus file (again)
for comparison purposes.   I'll either comment this code out or 
make it conditional on some property.

The comparison was successful 
for:

cipres_dist/help/samplefiles/TestNexusFile.nex
dna1.nex
dna2.nex
modified_from_hell.nex
cipres_dist/help/samplefiles/avian_ovomucoids.nex
protein1.nex

The comparison failed on rna1.nex because Mesquite seems to treat 
rna as dna. I saw code for handling RNA in Mesquite and a flag for
treating data as RNA in either DNAState.java or DNAData.java but
didn't look into how to enable it.

Some other things I noticied about Mesquite's handling of 
character data.  Mesquite seems to:

- convert explicit Ns in DNA matricies to ?
- (but) convert {ACGT} to N
- barf on {-ACGT}