NCLconverter - report of content of NEXUS file
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
- NCLconverter <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:
- nexus dnafasta aafasta rnafasta dnaphylip rnaphylip
aaphylip discretephylip dnaphylipinterleaved rnaphylipinterleaved
aaphylipinterleaved discretephylipinterleaved dnarelaxedphylip
rnarelaxedphylip aarelaxedphylip discreterelaxedphylip
aarelaxedphylipinterleaved discreterelaxedphylipinterleaved dnaaln rnaaln
aaaln phyliptree relaxedphyliptree nexml dnafin aafin rnafin
specifies the output file format expected:
- "normalized" NEXUS output
- Character data in fasta (could result in multiple output
- Trees and character data in phylip (could result in
multiple output files)
- Trees and character data in relaxed phylip (could result in
multiple output files)
- nexml output (this is also the default)
- -o<fn> specifies the output prefix.
- An appropriate suffix and extension are added
specifies the single output destination. Or you can use -d- to indicate
- 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!
- converts underscores to spaces in formats other than
translate to "safe" taxon names and store the new names as a
- 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"
use the NEXUS-formatted file called <filename> with a TaxaAssociation
- to restore original names.
- Assumes that the first taxa block in the
- block holds the original name and the second is the current
name. This function is useful for "undoing" the effects of the
- Suppress the creation of a NameTranslationFile
This manpage was written by Andreas Tille for the Debian distribution and can be
used for any other usage of the program.