NEXUSnormalizer - rewrites NEXUS file to standard out with
consistent indentation and syntax
NEXUSnormalizer takes reads a file and rewrites the file to
standard out with consistent indentation and syntax.
- NEXUSnormalizer <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
This manpage was written by Andreas Tille for the Debian
distribution and can be used for any other usage of the program.