I am using DNA sequences for phylogenetic analysis among plant species. I do not know how to root outgroup in cluster?
If you have calculated your tree in MEGA5 or 6 you can select the branch that covers your outgroup (cluster) and select on the left hand menue the tab with the green arrow head for "place root on branch". This will place the selected cluster at the bottom of your tree...
Dear Younas, Agreed with Stephen,
An outgroup can give you a sense of where on the bigger tree of life the main group of organisms falls. no matter where outgroup present in a phylogenetic tree, in middle or at base or top but the outgroup stems from the base of the tree. Just use a sequence which is distantly related to the other sequences in your tree. you can go through this link for clearing basic concept of outgroup with examples.
http://epidemic.bio.ed.ac.uk/how_to_read_a_phylogeny
If you have calculated your tree in MEGA5 or 6 you can select the branch that covers your outgroup (cluster) and select on the left hand menue the tab with the green arrow head for "place root on branch". This will place the selected cluster at the bottom of your tree...
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