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 flag).
- NCLconverter <path to NEXUS file>
-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
This manpage was written by Andreas Tille for the Debian
distribution and can be used for any other usage of the program.