NAME

       mkvtree - construct index for sequence

SYNOPSIS

       mkvtree [options]

DESCRIPTION

       The program mkvtree constructs an index for a given set of sequences. These are given as a list of input
       files. The sequences are referred to as database sequences. They can be over any given alphabet. The
       alphabet can be the DNA alphabet, or the protein alphabet, or any other alphabet consisting of printable
       characters. An alphabet is specified by a file storing a symbol mapping. The index consists of several
       files, the index files. Each such file stores a different table. The user specifies which tables (i.e.
       which part of the index) is written to a file, using one of eight output options, or a single option
       specifying that all tables are written to file.

       We support the following formats for the input files. They are recognized according to the first
       non-whitespace symbol in the file.

       •   multiple FASTA format: If the file begins with the symbol ">", then this file is considered to be a
           file in multiple FASTA format (i.e. it contains one or more sequences). Each line starting with the
           symbol ">" contains the description of the sequence following it. Each line not starting with the
           symbol ">" contains the sequence. Empty lines are allowed and ignored when reading the input.

       •   multiple EMBL/SWISSPROT format: If the file begins with the string "ID", then this file is considered
           to be a file in multiple EMBL format (i.e. containing one or more sequences, each in EMBL format).
           The information contained in the "ID" and "DE" lines is taken as the description of the corresponding
           sequence. The EMBL format is identical to the SWISSPROT format (w.r.t. the information we need to
           extract from such entries). So one can also use files in multiple SWISSPROT format as input.

       •   multiple GENBANK format: If the file begins with the string "LOCUS", then this file is considered to
           be a file in multiple GENBANK format (i.e. containing one or more entries in GENBANK format). The
           information contained in the "LOCUS" and the "DEFINITION" lines is taken as the description of the
           corresponding sequence.

       •   plain format: If the file does not begin with the symbol ">" or the strings "ID" or "LOCUS", then the
           file is taken verbatim. That is, the entire file is considered to be the input sequence (whitespaces
           are not ignored).

       There is no special option necessary to tell the program the sequence format. It automatically detects
       the appropriate format, according to the rules given above. If none of the above rules apply, then the
       program cannot recognize the input format and exits with error code 1. In such a case please check you
       input files for if they are conform with the input formats above. Another good solution is to use a more
       versatile sequence format transformation programs (e.g. readseq) to first generate multiple FASTA files
       and then feed this into mkvtree.

       Today many files containing sequence files are provided compressed by the program gzip. To simplify the
       use of these files, mkvtree also accepts gzipped input files. These files must have the ending ".gz". The
       gzipped formatted files are gunzipped internally and then processed as any other file.

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.

       -dna
           Input is DNA sequence.

       -protein
           Input is Protein sequence.

       -indexname <string>
           Specify name for index to be generated.

       -pl <length>
           Specify prefix length for bucket sort. Recommendation: use without argument; then a reasonable prefix
           length is automatically determined.

       -tis
           Output transformed input sequences (tistab) to file.

       -ois
           Output original input sequences (oistab) to file.

       -suf
           Output suffix array (suftab) to file.

       -sti1
           Output reduced inverse suffix array (sti1tab) to file.

       -bwt
           Output Burrows-Wheeler Transformation (bwttab) to file.

       -bck
           Output bucket boundaries (bcktab) to file.

       -skp
           Output skip values (skptab) to file.

       -lcp
           Output longest common prefix lengths (lcptab) to file.

       -allout
           Output all index tables to files.

       -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.

RETURNS

       If an error occurs, the program exits with error code 1. Otherwise, the exit code is 0.

SEE ALSO

       mkdna6idx(1)

                                                                                                      MKVTREE(1)