source: branches/stable/HELP_SOURCE/oldhelp/pa_bootstrap.hlp

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


TITLE           Estimation of Bootstrap by Parsimony

OCCURRENCE      ARB_PARSIMONY/Tree/Calculate Upper Bootstrap Limit

DESCRIPTION     Given a large tree, traditional ways to calculate bootstrap
                values are by magnitudes to slow. So a faster algorithm was
                developed:

                        the bootstrap value for each branch is calculated under
                        the assumption that all other branches have a 100% value.
                        Doing this we get an upper limit for the real bootstrap values.


NOTES           The program does not use the traditional Monte Carlo method to
                estimate the bootstrap values, but calculates them correctly
                under the assumption that the tree changes only locally.
                Try different filters and see the effect on the tree.

SECTION         ALGORITHM

                For each branch B do:

                      a                 b
                       \               /
                        >-------------<
                       /        B      \
                      c                 d

                exchange a with b ( or a with d ) and count all columns in the alignment
                with a greater/smaller/equal minimal number of mutations
                than the original tree.

                result:         n_plus, n_minus, n_equal
                                freq_n_plus = n_plus/ (seq_len)
                                ...

                Bootstrap value = sum of

                        for all i = 1.. seqlen do
                                for all combinations of np, nm,ne with np - nm == i do
                                        sum +=  freq_n_plus  ^ np *
                                                freq_n_minus ^ nm *
                                                freq_n_equal ^ ne *
                                                seq_len! / np! /nm! /ne!
                                done
                        done

SECTION         PUBLIC

                This algorithm is not published and I am not going to publish
                it. If you feel the strong need to do this, please don't forget
                to mention me (Oliver Strunk).

WARNINGS        Use filters to exclude superfluous gaps and to
                increase bootstrap values

BUGS            Does not work with weights
                Does not work with proteins