xenial (1) NCLconverter.1.gz

Provided by: ncl-tools_2.1.18+dfsg-2_amd64 bug

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.