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)

                                                                                                    MKDNA6IDX(1)