#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    subtopic.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           Column statistic 

OCCURRENCE      ARB_NT/SAI/Create SAI from Sequences/Positional Variability ...

DESCRIPTION     Calculates the base and frequencies positional variability for
                each column independently.

                It uses the parsimony method to find the minimum number of
                mutations for each site, as they are determined by the specified
                topology.

                The calculation is performed for sequences of all species in tree.
                For best results you should use one of the biggest trees available.
                The tree should have been optimized using ARB_PARSIMONY.

                The result can be used by:

                - Parsimony to weight the characters properly
                - Neighbour joining to estimate the distances more accurately.
                - Filter (read notes below)

                Resulting SAI will contain the following character codes:

                        '.'                          Less than 10% valid characters
                        '-'                          No mutations.
                        '0123456789ABCDE...'         Mutation rate category

                  The higher the digit/character of the mutation rate category is,
                  the more conserved the site is. Stepping 2 positions rightwards
                  in the list of given characters, approximately halves the mutation
                  rate (explicit mappings see below).

                Valid characters are "ACGTUacgtu" for DNA/RNA (or all amino acid codes for AA sequences).

NOTES           Opposed to consensus- and max-frequency-SAIs, the positional variability SAI
                is calculated based on the specified topology.

                Later that PVP-SAI might be used as an filter to further optimize that topology.
                When you filter out columns with high variability, topology changes that imply
                an increased number of mutations in these columns will receive no penalty.

                Repeating several iterations of these 2 steps might lead to a systematic error:
                 * variable columns will tend to become even more variable and
                 * conserved columns will tend to become even more conserved.

                The systematic error caused by this effect will probably mostly
                emphasize topological errors of the initial tree.
                To avoid that problem a tree should as well be optimized using other filters
                (e.g. max-frequency). This is especially true for the initial tree optimization.

WARNINGS        if you only have small trees (<100 species),
                using this function makes not much sense.

SECTION         Mapping of site mutation rate to categories: 

                    mutation rate      category

                    45.8% .. 75%          0     (max. possible mutation rate is ~75%)
                    36.5% .. 45.8%        1
                    28.2% .. 36.5%        2
                    21.3% .. 28.2%        3
                    15.7% .. 21.3%        4
                    11.5% .. 15.7%        5
                     8.3% .. 11.5%        6
                     6.0% ..  8.3%        7
                     4.3% ..  6.0%        8
                     3.1% ..  4.3%        9
                     2.2% ..  3.1%        A
                     1.5% ..  2.2%        B
                     1.1% ..  1.5%        C
                     0.78% .. 1.1%        D
                     0.55% .. 0.78%       E
                     0.39% .. 0.55%       F
                     0.28% .. 0.39%       G
                     0.20% .. 0.28%       H
                     0.14% .. 0.20%       I

                    mutations/million  category

                     976 .. 1400          J
                     691 ..  975          K
                     489 ..  690          L
                     346 ..  488          M
                     245 ..  345          N
                     173 ..  244          O
                     123 ..  172          P
                      87 ..  122          Q
                      62 ..   86          R
                      44 ..   61          S
                      31 ..   43          T
                      22 ..   30          U
                      16 ..   21          V
                      11 ..   15          W
                       8 ..   10          X
                       6 ..    7          Y
                       1 ..    5          Z


BUGS            No bugs known
