The main idea of ARB is to manage database access via a tree.
[ You don't have a tree, but you may access all species data using 'Species/Search and Query'. ]
There are several ways to construct an initial tree:
Align the sequence data:
Mark all 'species' (see ´Glossary´) Choose the item 'Mark all Species' from the menu 'Species' of the 'ARB_NT' main window (this program) (normally this is referred as: 'ARB_NT/Species/Mark all Species');
Select an alignment: <ARB_NT/3rd big Button in top area> (see ´Select an Alignment´)
To align the marked sequences use one of the provided aligners in 'ARB_NT/Sequence/Align Sequences'
Reconstruct an initial tree:
To get a good tree, you should use different treeing methods.
To quickly get an initial tree we recommend to use neighbour joining for DNA, RNA and Protein sequences:
To start neighbour joining select 'ARB_NT/Tree/Build tree from sequence data/Distance matrix methods/ARB Neighbor Joining', to display the 'NEIGHBOUR JOINING [ARB_DIST]' window. Refer to ´Neighbour joining´
for setting parameters of tree reconstruction.
Show the reconstructed tree:
Click on the <tree_*> (2nd big rectangular) button in top area of ARB_NT and choose the respective tree.
Choose the 'Save Whole Database as' item from the 'File' menu.