Reading Frames

Many analyses require that the open reading frames of the loci be known.  The 'Reading Frames' dialog allows you to set these and can be reached from the 'Options' menu.  The position of the first nucleotide of each open reading frame may be entered manually by selecting the appropriate option boxes or by pressing 'Autodetect'.  The autodetect function scans the sequences for stop codons in the three forward frames.  If there are more than one open reading frame for any set of sequences, the lowest nucleotide position is chosen as the start.  The program will remember these reading frames the next time the program starts.

reading frames dialog

Any analysis that requires the identification of the reading frames will prompt for this information and offer the opportunity to be taken to this dialog automatically.