NEXUSnormalizer - rewrites NEXUS file to standard out with consistent
indentation and syntax
NEXUSnormalizer takes reads a file and rewrites the file to standard out with
consistent indentation and syntax.
- NEXUSnormalizer <path to NEXUS file>
the command line shows this help message
suppress NCL status messages while reading files
reads a file and treats each line of the file as a path to NEXUS file
output AltNexus (no translation table in trees)
NOT validate internal labels in trees as taxa labels
NOT treat numbers in trees as taxon numbers, treat them as arbitrary
- labels (should not be used with NEXUS files).
integer> controls the NEXUS strictness level.
- the default level is equivalent to -s2 invoking the
program with -s3 or a higher number will convert some warnings into
fatal errors. Running with -s1 will cause the parser to accept
dangerous constructs, and running with -s0 will cause the parser
make every attempt to finish parsing the file (warning about very serious
- Note that when -s0 strictness level is used, and the
parser fails to finish, it will often be the result of an earlier error
than the error that is reported in the last message.
specifies the length of the interleaved pages to create
specifies the input file format expected:
- NEXUS (this is also the default)
- Amino acid data in fasta
- DNA data in fasta
- RNA data in fasta
- The complete list of format names that can follow the
-f flag is:
This manpage was written by Andreas Tille for the Debian distribution and can be
used for any other usage of the program.