NCLconverter(1)
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.
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