ARB Parsimony cannot be used to completely reconstruct new trees.
Existing trees can be optimized at different levels (depths) according to maximum parsimony criteria.
New sequences (species) can be placed rapidly into an existing tree. This can be done without changing that tree or allowing optimization at different levels according to maximum parsimony criteria including the new information for calculation.
The different ways to add species are explained in ´Add species without optimizing topology´
. Standard 'quick add' is available in this menu. To customize behavior or to optimize trees you have to start ARB parsimony in interactive mode.
Filters for the in- or exclusion of alignment columns ('ARB_NT/SAI; ARB_NT/Tree/Dist Matrix) can be selected.
After selecting one of the parsimony items in 'Tree/Add species to existing tree' the 'SET PARSIMONY OPTIONS' window appears:
Select the tree (to be modified) from the 'Tree:' subwindow.
Select an 'alignment' (see ´Glossary´) from the 'alignment:' subwindow.
To select a filter display the 'Select Filter' window pressing the button after the 'Filter:' prompt (see ´Select Filter´).
Press the <GO> button to display the 'ARB_PARSIMONY' window.