#       main topics:
UP      arb.hlp
UP      glossary.hlp

#       sub topics:
SUB     partial_sequences.hlp
SUB     pa_quick.hlp
SUB     pa_add.hlp

# format described in ../help.readme


TITLE		Add marked partial species

OCCURRENCE	ARB_PARSIMONY/Tree/Add Species to Tree/Add Marked Partial Species

DESCRIPTION     Use this to add sequences with partial sequence data into an existing tree.
                The current tree topology will not be optimized after insertion.

                The branchlengths of the added partial sequences represent the
                number of (weighted) mutations against the full sequence.

                Only the overlapping part of both sequences is taken into account and
                the distance to the FLS will be weighted by the length of the overlap.

                Different partial sequences will never attract each other, simply because
                they are not considered as 'possible neighbours' (see also section about
                partials in LINK{pa_quick.hlp}).

                As for non-partial sequences, when using a filter only the unfiltered
                positions will be taken into account to calculate the number of mutations.

                The insertion order has no effect on the resulting placement of the
                partial sequences. For each sequence, the best matching
                full-length sequence (FLS) is searched and afterwards all partial
                sequences are placed next to their detected FLS.

                Often partial sequences have equal distances to more than one FLS. This happens
                whenever two FLS only differ in alignment regions, where the partial sequence has
                no data. In that case a warning is printed ("Insertion of '<name>' is ambiguous")
                and one of the ambiguous insertion possibilities is chosen.
                This is more likely to happen for low amounts of sequence data (i.e. very short sequences).
                Consider to remove these species from the tree, as their placement might be
                meaningless or misleading.

NOTES		Adding species using this function marks them as "partial sequence" if
                they have no 'ARB_partial' entry yet.
                If they were already marked as FLS, the insertion is aborted with an error.

                All species already in tree, when calling this function, will be marked
                as FLS, if they have no 'ARB_partial' entry yet.

                Species with partial sequences have the field "ARB_partial" set to 1, species
                with FLS have the field "ARB_partial" set to 0.

EXAMPLES	None

WARNINGS	Calculating branch length after adding partial sequences
                will lead to wrong lengths.

BUGS		No bugs known
