Phylogenetic Tree

Question

[Nisa]

frens, i wanna ask u bout neighbour-joining tree (PHYLIP version) .. my OUTGROUP that i choose to be the root were always in INGROUP. why these happened? n wat should i do to get the outgroup for the tree? for the root... tq

Answer 1

[Bill Pearson]

Use the "retree" program in the phylip package to set the outgroup and the root.

[Nisa]

dear Pearson... thank you so much.. but can u explain more? yes, i have the retree software in my phylip folder... but, stil dont know how to set outgroup and the root..

i did not understand about the command to press node number of OUTGROUP.... when i press the node number at OUTGROUP, it will say....."not a possible option!"....................... why?

Answer 2

[Bill Pearson]

To set the outgroup with "retree", you need to press 'o' and then the number of the taxon you wish to use as the out group.

Another handy command in 'retree' is 'm', which uses "mid-point" rooting.

When you are done, be sure to save the tree (it will be named 'outtree' if that file does not exist already).

[Nisa]

got it.. tq soooooo much :)