The nexus file might has the wrong format. While most of the nexus files
can be processed by the CAOS-Analyzer some formats lead to error.
For correct output it is crucial that the nexus file contains an alignment of
sequences followed by a tree based on this sequences.
Following formats are known to cause errors when used with CAOS:
1) Please check if your nexus file includes an interleaved seuquence
matrix. The "interleaved" format is not supported by the Analyzer.
MacClade (File->Options for Saving->NEXUS Format):
2) Please control your sequence names. Multiple names should be connected by an
underline character "_". Hyphenate multiple names can also cause error.
3) Use only dichotomal trees in the nexus file! The current version of CAOS can only
process dichotomal branching points and will only process two branches at a polytomal
branching point. CAOS will ingnore the remaining branches!
4) Use only unique sequences in a CAOS-Analyzer analyses. Adding multiple sequences
with identic characters will not improve the barcode output and might cause problems
when using the output of the CAOS-Analyzer in the CAOS-Barcoder.
If you observe an error that is not listed above please feel free to contact us
so we can either fix the problem or address the issue.