Dear Users,
I used 3 different but closely related protein groups, and done Phylogenetic tree analysis by using 2 method i.e. neighbor-joining and maximum-likelihood method with 1000 replicates using MEGA6.
In both the tree obtained, in one tree (neighbor-joining) it is showing protein group 1 is similar to protein group 2, in other tree (maximum-likelihood) protein group 1 is similar to protein group 3.
Can anyone explain about how two tree method showing different tree and what is its significance.
Thanks
Shashank
Thank you for your quick reply.
I did using Bootstrap method with 1000 replicates, others parameters were set default. Model/Method used Jones-taylor-Thornton (JTT) model. This is for academic purpose, I am not looking for publication -quality phylogentic tree. Though I have seen in many Research paper, they used MEGA software for Phylogenetic tree