I am an amateur or beginner in the field of bioinformatics. Related to one of my recent projects I need one help.
I used McGee Y utility software to calculate Genetic Distance for the Y DNA data obtained from FTDNA. With the output file in phylip format I created a phylogenetic tree using MEGA v6. I need to put the scaling in years in the phylogenetic tree (as found in the HAM project- link given). Can anyone help me by telling how to calculate and represent these kind of scale in a phylogenetic tree. Is this by approximately putting values using the data got from Time to most recent common ancestor table or from any other calculation?
Kindly note the scale bar given in years (Years ago) at the bottom of the phylogenetic tree http://home.earthlink.net/~odoniv/HamCountry/HAM_DNA_Project/HAM_DNA_charts.html
There are molecular clock functions in MEGA, not sure if those apply here. Do you know the divergence times already, or do you want to calibrate the tree? If you built your tree from a distance matrix, I am not sure it makes a difference if the calibration is in million years ago or years.
Thanks for your quick response. I already made the tree using Y-DNA marker values taken from Family tree DNA with the help of McGee Y utility program. Now just need to put an indication like how many years before a common ancestor existed. So is it possible to get an idea of that from any of the data got from McGee Y utility program.
You need some calibration points for some branches in your topology. I think you just have to get some reliable estimates.