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UP      arb_pars.hlp
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# format described in ../help.readme


TITLE		Parsimony value

OCCURRENCE	displayed in the top area of the ARB_PARSIMONY main window

DESCRIPTION     The parsimony value indicates the
                quality of a trees topology.

                Basically it counts the minimum number of base mutations that
                necessarily needed to occur,
                if we assume that the current topology represents the way the evolution took.
                Therefore smaller values indicate better topologies.

                Several parameters influence the absolute parsimony value:

                - if you specify a filter (in parsimony startup window) only mutations
                  in the remaining, unfiltered alignment columns are counted, i.e. filtering
                  will normally lower the resulting parsimony value.
                - if you specify a weighting mask (in parsimony startup window) higher
                  weighted sites will count stronger and raise the absolute parsimony value.
                - adding more species to a tree will normally raise the number of mutations,
                  i.e. a tree with many species has a higher parsimony value than a tree
                  with fewer species (see also LINK{pa_reset.hlp}).

                If you compare parsimony values of different topologies you need to use
                the same alignment, the same filter, the same weighting mask and the
                same set of species.

SECTION         Dots

                ARB uses dots ('.') as a special gap type.
                The meaning of a dot is "might be a gap or a nucleotide/aa".
                It indicates the lack of any information about the sequence data at the
                position where they are used.

                Opposed to that, a normal gap ('-') clearly states that it is KNOWN that the
                sequence does NOT CONTAIN any bases at the positions of the gaps - the gaps have
                only been inserted for alignment purposes.

                And - opposed to gap - a 'N' (or 'X' for amino acid sequences) clearly states,
                that it is KNOWN that the sequence CONTAINS some nucleotide/aa at that position.

                In ARB databases you should use dots at both ends of the alignment.
                Doing so means: you know that the sequence continues in both directions - it just
                has not been sequenced completely.

                Also you may use dots in the middle of the alignment, whenever you have
                stronger indications, that some gap might in fact be a sequencing error.

SECTION         Mutations against dots

                When the parsimony value is calculated, dots do not cause mutations.
                They will match any base or gap or other dot.

                That means, dots at both sequence endings will compensate some of the
                negative effects, that are normally caused by using sequences of different
                lengths (e.g. clustering of LINK{partial_sequences.hlp}).


SECTION         Differences between sequence types

                For nucleotide sequences:

                    Mutations are simply counted for single nucleotides.

                For amino acid sequences:

                    Mutations are determined on amino acid basis. This differs
                    from what would be done when using the corresponding
                    DNA alignment:

                    - in DNA several different codons (combinations of 3 nucleotides)
                      may represent the same amino acid. Therefore a mutation would
                      be counted for DNA, where no mutation is counted for AA.
                    - the parsimony value for amino acid alignments does not count
                      the number of amino-acid-mutations. It counts the minimum
                      number of nucleotide(!) mutations needed to mutate from one
                      amino acid to another, while assuming that there is no
                      selection pressure when mutating a codon into another codon that
                      translates into the same amino acid (see also EXAMPLES below).

                    ARB generally uses the "Standard code" to calculate the
                    mutations between different amino acids, when determining
                    the parsimony value.

NOTES		The parsimony value is also used to LINK{pa_branchlengths.hlp}.

EXAMPLES	for an amino acid mutation

                Imagine an alignment position P and three species, where

                 - species F has an 'F' (Phenylalanine) at position P,
                 - species Q has a 'Q' (Glutamine) at position P and
                 - species L has an 'L' (Leucine) at position P.

                These amino acids may be represented by the following codons:

                 - F = TTT | TTC
                 - Q = CAA | CAG
                 - L = TTA | TTG | CTN

                Based on the minimum codon distances, the mutation costs used
                in ARB_PARSIMONY are:

                 - F -> Q = 3 mutations
                 - F -> L = 1 mutation (e.g. TTT -> TTA)
                 - L -> Q = 1 mutation (e.g. CTA -> CAA)

                This results in the following parsimony values for the
                possible subtree-rearrangements (R=Rest of whole tree):

                         R
                         |
                         |
                         F              pars value = 4
                        / \
                       /   \
                      Q     L


                         R
                         |
                         |
                         Q              pars value = 4
                        / \
                       /   \
                      F     L


                         R
                         |
                         |
                         L              pars value = 2 (!)
                        / \
                       /   \
                      Q     F


                Assuming the third topology (which is the "best" according to the parsimony
                value), means to assume that the ancestor of Q and F had an L at position P.
                As no selection pressure is assumed for mutating that 'L'-codon (e.g.
                from 'TTA' into 'CTA') no mutation penalty is counted when calculating the
                parsimony value.

WARNINGS	None

BUGS		No bugs known
