Implement --outgroup correctly.

[xflouris]

Remove the option --outgroup and create two new options:

• --outgroup_taxa TAXA
• --outgroup_crop

  --outgroup_taxa

The first option specifies the taxa of the outgroup and accepts a comma-separated list of taxa. For unrooted trees all taxa of a subtree must be specified in order to select a unique subtree, or the specific case of one taxon can also be specified. This option will root the unrooted tree at this outgroup. For the case of rooted trees, any number of taxa will suffice, and the option will have no effect unless --outgroup_crop is specified.

--outgroup_crop

Crops the outgroup from the rooted or unrooted tree at the point of the most recent common ancestor specified by --outgroup_taxa.

[xflouris]

started work on this

[xflouris]

finished