I am using the bioperl Bio::AlignIO module to create some nexus files, to run with mrbayes.
When I try to execute a nexus file created with bioperl I get the error:
Could not find parameter "symbols"
The problem is that bioperl Bio::AlignIO::Nexus creates a nexus file with the parameter 'symbols' after the format, gap and interleave declarations.
The 'symbols' parameter describes the symbols used in the files, e.g. 'ACTGN' for DNA sequences.
You can try by executing the attached nexus file with mrbayes 3.1.2.
I am using mrbayes on a linux platform.