setting outgroup

[grenaud]

I tried

` ./newick_v1.0.1429_linux in.treefile -outGroup outgroup -output rooted.newick

Invalid command line
Expected -option_name or --option_name, got 'in.treefile'

`

[rcedgar]

-outGroup should be -outgroup

[grenaud]

sorry yes you are right but I still get the same error.

[rcedgar]

you are missing command name in the command line, it should be either

newick -rootbyoutgroup unrooted.newick -outgroup clade_label -output rooted.newick

where clade_label is matched by substring, or

newick -rootbyoutgroup unrooted.newick -labels clade_labels.txt -output rooted.newick

[grenaud]

ok I am actually trying to generate a new tree where I substitute entire subtrees for a single leaf, is this possible? It was complaining that my tree was not rooted.

[grenaud]

and the -rootbyoutgroup has worked.

[rcedgar]

newick does not have a command to do this.