NAME

       NEXUSnormalizer - rewrites NEXUS file to standard out with consistent indentation and syntax

DESCRIPTION

       NEXUSnormalizer  takes reads a file and rewrites the file to standard out with consistent indentation and
       syntax.

   The most common usage is simply:
              NEXUSnormalizer <path to NEXUS file>

OPTIONS

       -h on the command line shows this help message

       -q suppress NCL status messages while reading files

       -l<path> reads a file and treats each line of the file as a path to NEXUS file

       -a output AltNexus (no translation table in trees)

       -x do NOT validate internal labels in trees as taxa labels

       -X do NOT treat numbers in trees as taxon numbers, treat them as arbitrary

              labels (should not be used with NEXUS files).

       -s<non-negative 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 errors).

              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.

       -i<number> specifies the length of the interleaved pages to create

       -f<format> specifies the input file format expected:

       -fnexus
              NEXUS (this is also the default)

       -faafasta
              Amino acid data in fasta

       -fdnafasta
              DNA data in fasta

       -frnafasta
              RNA data in fasta

              The complete list of format names that can follow the -f flag is:

              nexus
              dnafasta
              aafasta
              rnafasta
              dnaphylip
              rnaphylip
              aaphylip
              discretephylip
              dnaphylipinterleaved
              rnaphylipinterleaved
              aaphylipinterleaved
              discretephylipinterleaved
              dnarelaxedphylip
              rnarelaxedphylip
              aarelaxedphylip
              discreterelaxedphylip
              dnarelaxedphylipinterleaved
              rnarelaxedphylipinterleaved
              aarelaxedphylipinterleaved
              discreterelaxedphylipinterleaved
              dnaaln
              rnaaln
              aaaln
              phyliptree
              relaxedphyliptree
              nexml
              dnafin
              aafin
              rnafin

AUTHOR

       This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage
       of the program.