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Main topics: ARB: a Short Introduction Glossary What are Marked Species? | Related topics: Select an Alignment Neighbour joining
# How to get an initial tree DESCRIPTION NOTES WARNINGS BUGS ## DESCRIPTION
### 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. ### Save everything: Choose the 'Save Whole Database as' item from the 'File' menu.
## NOTES
### None
## WARNINGS
### None
## BUGS
### No bugs known