---
name: "NCLconverter"
section: "1"
platform: "linux"
package: "ncl-tools"
version: "2.1.21+git20210811.b1213a7-6"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/NCLconverter"
---

# NCLconverter(1)

report of content of NEXUS file

## 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.