NAME

       trainphd - interpretation of DNA Sanger sequencing data

DESCRIPTION

       -h     (Help) This message

       -C <consensusfile>
              Specify the name of the FASTA file which contains the consensus sequence

       -V <vector>
              Specify the name of the FASTA file which contains the vector sequence

       -P <primer>
              Specify the name of the FASTA file which contains the primer sequence

       -S <site>
              Specify the name of the FASTA file which contains the restriction site sequence

       -M <match>
              Specify the match premium     (default is 10)

       -X <mismatch>
              Specify the mismatch penalty  (default is 20)

       -G <gap_penalty >
              Specify the gap initiation or extension penalty (default is 40)

       -r <repeat_fraction>
              Specify the repeat_fraction   (default is 0.85)

       -f <max_frac_of_err>
              Specify  the allowable fraction of errors within the best alignment region. Default
              is 0.1. If actual fraction of errors  exceeds  this  vale,  the  fragment  will  be
              rejected (=not used in training process)

       -a <min_portion_aligned> Instructs trainphd to ignore a read if less than
              the  specified  portion of its bases is aligned with reference sequence (default is
              0)

       -l <min_read_length>
              Instructs trainphd to ignore a  read  of  length  less  than  specified  number  of
              basepairs (0 by default)

       -o <output_file>
              Specify the name of the output file. By default, the output will be made to stdout

       -t <tab_dir>
              Instructs  trainphd  extract  alternative  base  calls  from  TAB  files  stored in
              directory tab_dir and to output these calls, together with quality value  for  each
              alternative call

       -d <dir>
              Read the input PHD files from specified directory

       -j <projectfile>
              Specify  the  name of the projectfile which comprises two columns: the full path to
              the FASTA file which contains the consensus sequence, followed by the full path  to
              the sample file

AUTHOR

       This  manpage was written by Andreas Tille for the Debian distribution and can be used for
       any other usage of the program.