Hi,

I am trying to draw phylogenetic tree for a particular gene family using available online tools such as tree view, ITOL. The tree includes 6 fungal pathogens, 3 model plant genomes i.e arabidopsis, rice, and brassica and 1 yeast genome. The tress is out of clustalx 2.0 using default options and I am using .dnd and .phb (1000 bootstrap).

Now, I am not getting the desired output as I was expecting the gene family from plant should be form one clan, yeast should be in different clan and rest in 1 clan. I do not know what is going wrong in this tree. I am not sure if I am doing the analysis in right way or I must obsolete or include some data to get it what I want.

Or what could be possible explanation for such output.