---
name: "mkdna6idx"
section: "1"
platform: "linux"
package: "vmatch"
version: "2.3.1+dfsg-9"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/mkdna6idx"
---

# mkdna6idx(1)

generate a six frame translation index

## NAME

mkdna6idx - generate a six frame translation index

## SYNOPSIS

**mkdna6idx** \[options\] \<indexname\>

## DESCRIPTION

**mkdna6idx** is very similar to **mkvtree**. While **mkvtree** can handle sequences over arbitrary alphabets, **mkdna6idx** requires DNA-sequences as input. It generates two indices, namely:

• A flat index "indexname" for the the given DNA sequences. It mainly consists of the two files "indexname.tis" and "indexname.ois". This index is mainly used for output purpose.

• An index "indexname.6fr" for the given DNA sequences translated in all six reading frames.This is used for computing the matches.

Please also see the Vmatch manual for a more detailed explanation of the usage.

## OPTIONS

- **-db** \<file\>

  Specify database files (mandatory).

- **-smap** \<file\>

  Specify file containing a symbol mapping. This describes the grouping of symbols. It is possible to set the environment variable MKVTREESMAPDIR to the path where these files can be found.

- **-transnum** \<table\>

  Perform six frame translation. Specify codon translation table by a number in the range \[1,23\] except for 7, 8, 17, 18, 19 and 20; (default is 1):

  ```
   1 Standard
   2 Vertebrate Mitochondrial
   3 Yeast Mitochondrial
   4 Mold Mitochondrial; Protozoan Mitochondrial; Coelenterate Mitochondrial; Mycoplasma; Spiroplasma
   5 Invertebrate Mitochondrial
   6 Ciliate Nuclear; Dasycladacean Nuclear; Hexamita Nuclear
   9 Echinoderm Mitochondrial
  10 Euplotid Nuclear
  11 Bacterial
  12 Alternative Yeast Nuclear
  13 Ascidian Mitochondrial
  14 Flatworm Mitochondrial
  15 Blepharisma Macronuclear
  16 Chlorophycean Mitochondrial
  21 Trematode Mitochondrial
  22 Scenedesmus Obliquus Mitochondrial
  23 Thraustochytrium Mitochondrial
  ```

- **-indexname** \<string\>

  Specify name for index to be generated.

- **-cpl**

  Use reverse complement of the input sequence.

- **-tis**

  Output transformed input sequences (tistab) to file.

- **-ois**

  Output original input sequences (oistab) to file.

- **-maxdepth** \<len\>

  Restrict the sorting to prefixes of the given length.

- **-v**

  Verbose mode.

- **-version**

  Show the version of the Vmatch package

- **-help**

  Show help.

## SEE ALSO

[mkvtree(1)](/mkvtree/1.md)