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# Estimation of Bootstrap by Parsimony

## 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.

## 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```