1. When you have opened your dataset in MEGA5 (Sequence Data Explorer), click the tab 'data' and then 'select and edit taxa and groups'.

2. group your samples of each species, so that each group represents a species

3. in the main menu, select 'distance' and then 'compute within-group mean distance' and 'compute between group mean distance'.

Please have a look at my publication http://www.hindawi.com/journals/tswj/aip/793414/

the best software to calculate intra- and inter-species variation is Arleqin 3.5

if you need further assistance, contact me

1. When you have opened your dataset in MEGA5 (Sequence Data Explorer), click the tab 'data' and then 'select and edit taxa and groups'.

2. group your samples of each species, so that each group represents a species

3. in the main menu, select 'distance' and then 'compute within-group mean distance' and 'compute between group mean distance'.

Immense thanks @Farhat Ahmadi Avin and @George Sangster for your kind advice.

This is great! Can I just ask how you then calculate the percentage variance from the table you're presented with when you've done that? Thank you!

If you are using MEGA the best way is to export it as excel file and from there you can calculate Variance, standard deviation and standard error.

Thank you Shahed for asking the question and thanks to those who responded. I had the same question too, just got introduced to phylogenetics and  I am trying to learn the concept myself.