# mkdna6idx(1)

## 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)
