- System.out.println( " " + PRG_NAME + " my_tree.nh result.tsv" );
- System.out.println( " " + PRG_NAME + " -c=0.5 -s=. my_tree.nh result.tsv" );
- System.out.println( " " + PRG_NAME + " -c=0.9 -s=_ -m=map.tsv my_tree.nh result.tsv" );
- System.out.println( " " + PRG_NAME + " -x -xs=& -xk my_tree.nh result.tsv" );
- System.out.println( " " + PRG_NAME + " -x -xs=\"|\" my_tree.nh result.tsv" );
- System.out.println( " " + PRG_NAME + " -x -xk -m=map.tsv pplacer_out_trees.sing.tre result.tsv" );
+ System.out.println( " " + PRG_NAME + " pp_out_tree.sing.tre result.tsv" );
+ System.out.println( " " + PRG_NAME + " -c=0.5 -s=. pp_out_tree.sing.tre result.tsv" );
+ System.out.println( " " + PRG_NAME + " -c=0.9 -s=_ -m=map.tsv pp_out_trees.sing.tre result.tsv" );
+ System.out.println( " " + PRG_NAME + " -x -xs=& -xk pp_out_trees.sing.tre result.tsv" );
+ System.out.println( " " + PRG_NAME + " -x -xs=\"|\" pp_out_trees.sing.tre result.tsv" );
+ System.out.println( " " + PRG_NAME + " -x -xk -m=map.tsv pp_out_trees.sing.tre result.tsv" );