NAME

       NCLconverter - report of content of NEXUS file

DESCRIPTION

       NCLconverter  takes  reads  a  file  and  writes  a report of the content to a file prefix
       (specified with the -o flag) in the chosen output format (specified with the -e flag).

   The most common usage is simply:
              NCLconverter <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

       -e<format> specifies the output file format expected:

       -enexus
              "normalized" NEXUS output

       -efasta
              Character data in fasta (could result in multiple output files)

       -ephylip
              Trees and character data in phylip (could result in multiple output files)

       -erelaxedphylip
              Trees and character data in relaxed phylip (could result in multiple output files)

       -enexml
              nexml output (this is also the default)

       -o<fn> specifies the output prefix.
              An appropriate suffix and extension are added

       -d<fn> specifies the single output destination. Or you can use -d- to indicate that

              output  should be directed to standard output.Warning use of this option may result
              in an invalid output due to concatenation of separate "blocks" of information  into
              a single file!

       -u     converts underscores to spaces in formats other than NEXUS.

       -y<filename> translate to "safe" taxon names and store the new names as a NEXUS.

              file  called  <filename>  with a TaxaAssociation block. The first taxa block in the
              association block will hold the original names, and the second will hold the "safe"
              names

       -Y<filename> behaves like -y, except with -Y a translation file will be produced even
              if the original names were already "safe"

       -z<filename> use the NEXUS-formatted file called <filename> with a TaxaAssociation block

       to restore original names.
              Assumes that the first taxa block in the TaxaAssociation

              block  holds the original name and the second is the current name. This function is
              useful for "undoing" the effects of the -y option.

       -j     Suppress the creation of a NameTranslationFile

AUTHOR

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