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NEXUSnormalizer - rewrites NEXUS file to standard out with consistent

NEXUSNORMALIZER(1) User Commands NEXUSNORMALIZER(1)

NAME

NEXUSnormalizer - rewrites NEXUS file to standard out with consistent indentation and syntax

DESCRIPTION

NEXUSnormalizer takes reads a file and rewrites the file to standard out with consistent indentation and syntax.

The most common usage is simply:

NEXUSnormalizer <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

AUTHOR

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
January 2016 NEXUSnormalizer 2.1.18