NAME

       convert_coords  -  converts  coordinates of features in a GFF file according to a multiple
       alignment

DESCRIPTION

       Converts coordinates of features in a GFF file according to a  multiple  alignment.   Will
       map  from  the coordinate system of any sequence to any other sequence; can also map to or
       from the coordinate system of the entire alignment.  In addition, supports translation  of
       coordinates by specified offset.

OPTIONS

       -m <msa_fname>
              (required) Name of file in which alignment is defined.

       -f <gff_fname>
              (required) Name of file in which features are defined (GFF).

       -s <src_frame>
              Index  of  frame  of reference for feature coordinates, as defined in the GFF file.
              Use an integer 1-N (if N seqs) or 0  to  indicate  the  coordinate  system  of  the
              alignment  as  a  whole.   Default  behavior  is  to  match features with alignment
              sequences by name (feature by feature).  -d <dest_frame> Index of destination frame
              of  reference.   Default  is  0  (whole  MSA).   -p <coord_off> Positive coordinate
              offset.  This value will be added to all coordinates.  Useful  when  the  alignment
              (or  sequence) for which the coordinates are specified is a sub-alignment of yours.
              -n <coord_off> Negative coordinate offset.  This value will be subtracted from  all
              coordinates.   Useful  when  your alignment is a sub-alignment of the alignment (or
              sequence)  for  which  the  coordinates  are  specified.   -i   FASTA|PHYLIP|MPM|SS
              Alignment format.  Default is to guess format from file contents