NAME

       gt-eval - Compare annotation files and show accuracy measures (prediction vs. reference).

SYNOPSIS

       gt eval reference_file prediction_file

OPTIONS

       -nuc
           evaluate nucleotide level (memory consumption is proportional to the input file sizes) (default: yes)

       -ltr
           evaluate a LTR retrotransposon prediction instead of a gene prediction (all LTR_retrotransposon
           elements are considered to have an undetermined strand) (default: no)

       -ltrdelta
           set allowed delta for LTR borders to be considered equal (default: 20)

       -v
           be verbose (default: no)

       -o
           redirect output to specified file (default: undefined)

       -gzip
           write gzip compressed output file (default: no)

       -bzip2
           write bzip2 compressed output file (default: no)

       -force
           force writing to output file (default: no)

       -help
           display help and exit

       -version
           display version information and exit

DESCRIPTION

       The program shows sensitivity and specificity values for certain feature types (e.g., gene, mRNA, and
       exon). For some feature types the number of missing and wrong features of that type is also shown.
       Thereby, “missing” means the numbe r of features of that type from the “reference” without overlap to a
       feature of that type from the “prediction”. Vice versa, “wrong” denotes the number of features of that
       type from the “prediction” without overlap to a feature of that type from the “reference”.

AUTHOR

       Report bugs to <gt-users@genometools.org>.

                                                   10/07/2012                                         GT-EVAL(1)