Deciding an outgroup to root the tree

[Ram-Nagar]

Hi there,
I am not sure which sample I use an outgroup to root the tree. Is there any way to choose midpoint while converting a vcf file to phlylip using your script?
Thanks

[edgardomortiz]

There is no need to specify an outgroup, this feature just places that sample at the start of the alignment (since many phylogenetic programs will "root" the tree at the first sample). If you want midpoint you will have to provide an option to your phylogenetic software.

Edgardo