Phylogenetic Trees

Question

[int11ap1]

Good afternoon everyone!

I am meant to do a phylogenetic tree of 5 mitochondrial genomes. So, I first aligned these genomes using MAFFT. Then, using Gblocks, the divergent regions have been filtered. Using jModelTest, the evolutionary model has been estimated. Bootstrap 1000 times and finally my tree is done using PhyML.

However, I am completely lost about how to calculate the molecular clock and the evolutionary ratio. Any help?

Thanks!!

[David W]

To get a helpful answer you'll need to be more specific. How do you want to use a molecular clock (applying a known rate across a tree, or using known dates to infer the rate?) and what do you meant by "evolutionary ratio"?

Answer 1

[arnstrm]

This article should help you 'Phylogenetic Analysis of 47 Chloroplast Genomes Clarifies the Contribution of Wild Species to the Domesticated Apple Maternal Line'. Although it is for Chloroplast genomes, the methods should be almost similar.