NEXUSvalidator - Online in the Cloud

PROGRAM:

NAME

NEXUSvalidator - validate NEXUS file

DESCRIPTION

NEXUSvalidator takes reads a file and exits with a success (return code 0) if the file is
valid.

The most common usage is simply:
NEXUSvalidator <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.

-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

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