Hi,

I downloaded gg_13_5_otus_99_annotated.tree.gz from http://greengenes.secondgenome.com/downloads/database/13_5 which contains a newick tree of 16S RNA taxonomy. I would like to extract a simple phylogeny tree, for example the relation between g__Straphylococcus, g__Streptococcus and g__Enterococcus . The problem is for each species, there are too many leaves labeled with number, which probably correspond to sequences IDs.

     # This command print all nodes except leaves. I get all my taxonomy
     nw_labels -L gg_13_5_otus_99_annotated.tree 
     # Output : 
     s__sedula
     g__Metallosphaera
     g__Acidianus
     g__Stygiolobus
     s__metallicus
     g__Sulfolobus
     g__Sulfolobus 
     ......

    # This command print only leaves. I get a list of number 
    nw_labels -I gg_13_5_otus_99_annotated.tree 
    # Output : 
     550922
     1113159
     569299
     1106705
     1104518
     556057
     3119364

So I want to remove all leaves, to be able to get trees without sequence node.
Any idea using newick tools or something else ?