#Please insert up references in the next lines (line starts with keyword UP)
UP      arb.hlp
UP      glossary.hlp

#Please insert subtopic references  (line starts with keyword SUB)
SUB    realign_dna.hlp
SUB    translate_dna_2_pro.hlp

# Hypertext links in helptext can be added like this: LINK{ref.hlp|http://add|bla@domain}

#************* Title of helpfile !! and start of real helpfile ********
TITLE           Recommended way to maintain amino acid alignments

DESCRIPTION     how we handle AA/DNA databases:

                    1. we maintain a DNA alignment for ALL sequences we want in our
                       database.

                    2. we translate the DNA alignment into an amino acid alignment
                       => each species has 2 alignment entries,
                       e.g. "data/ali_dna" and "data/ali_pro"

                    3. we align the protein sequences

                    4. we realign DNA (according to the aligned protein sequences; see LINK{realign_dna.hlp})

                    Here some reasons why we act as described:

                    * we want to maintain a DNA alignment, to be able to use
                      the PT-Server (to find next relatives). You'll find a section
                      about that issue in LINK{faligner.hlp}.
                    * we want to keep DNA data, because it contains more information than the
                      translated protein sequences (you cannot create DNA from protein
                      sequences).
                    * we want to align sequences using protein alignments, because the
                      alignment of protein sequences is more determined than the alignment
                      of the corresponding DNA sequences.
                    * we always realign DNA after changing the protein alignment,
                      to always be able to perform a new translation from scratch (e.g. if
                      translation table changes; see LINK{translate_dna_2_pro.hlp})


NOTES           None

EXAMPLES        None

WARNINGS        None

BUGS            No bugs known