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# format described in ../help.readme


TITLE		Alignment adaption (select species)

                Select species to use for alignment adaption

OCCURRENCE	ARB_MERGE/TRANSFER SPECIES (Adapt alignment/SELECT)

DESCRIPTION     Helps you finding candidates for alignment preservation.

                Normally people have inserted new gaps in one of the two databases.
                ARB Merge tries to adapt the alignment.

                To be able to do this, you have to specify one or more species or SAIs
                existing in BOTH databases. ARB Merge then creates a column reference list
                and realigns all transferred species according to this list.

                Press the 'Find candidates' button to search both databases for candidate
                species/SAIs and rate them.

                A list of species/SAIs shows up. The first column contains the name,
                the second column the number of alignments containing data for this species/SAI,
                the third column shows the position-count-difference (see below),
                the fourth column is the score (higher value means better).

                The list is sorted by score, i.e. best candidates are listed at the top.

                The term 'position-count-difference' is calculated like follows:
                For all alignments the number of non-gaps (i.e. neither '-' nor '.') are counted and
                the differences between these counts are summarized for all alignments.
                Best value is 0, which normally means the sequence data of the species (or the SAI data)
                didn't change. A high value means that species changed data and isn't a good candidate
                for alignment preservation.

                To enable this feature, enable the 'Adapt alignment' toggle.

NOTES		In our database releases we provide SAIs named 'gaps_...'.
                These SAIs are the best candidates for alignment preservation.

                When merging similar databases with many species, searching adapt candidates
                may take a long time. Press KILL in the status window to abort the process.

EXAMPLES	None

WARNINGS	Calculated SAIs (like MAX_FREQUENCY or POS_VAR_BY_PARSIMONY) show up on top
                but they are normally NO good candidates for preservation.

BUGS		No bugs known
